South Sudanese presidential representative Barnaba Marial Benjamin (L) and Thomas Cirillo Swaka, member of the South Sudan Opposition Alliance (SSOMA), meet at the Community of Sant'Egidio's International Relations headquarter in Rome on 14 October 2020. FILIPPO MONTEFORTE / AFP
Briefing / Africa 20+ minutes

South Sudan’s Other War: Resolving the Insurgency in Equatoria

A rebellion in Equatoria, South Sudan’s southernmost region, is undermining the already troubled peace between the main belligerents in its civil war. Mediators should push for a wider compact that accommodates Equatorian grievances and includes the insurgent general in talks about the country’s political future.

What’s new? Despite a 2018 deal bringing South Sudan’s main warring parties into a ceasefire and unity government, a rebellion in the southern multi-ethnic Equatoria region fights on. Its leader, Thomas Cirillo, rejects the agreement, saying it fails to address his peoples’ core grievances, while calling for greater autonomy from the centre.

Why does it matter? On-and-off fighting is cutting a swathe of destruction in Equatoria, including south and west of the capital Juba, displacing hundreds of thousands of people into neighbouring countries and obstructing South Sudan’s path out of war and toward a more viable future.

What should be done? Mediators and external powers should press Cirillo and South Sudanese President Salva Kiir to broaden the existing peace deal by fulfilling the bespoke ceasefire agreement between them. Cirillo should join the country’s constitution-making process. Parties also should support a grassroots process to address local grievances.


I. Overview

South Sudan’s long civil war is not over, as a major insurgency south and west of the capital Juba has plunged large parts of the Equatoria region into chronic bouts of violence that have displaced many thousands. A February 2018 pact bringing South Sudanese President Salva Kiir and his rival First Vice President Riek Machar into a ceasefire and unity government was a major step forward in ending the war. Yet the holdout rebellion in Equatoria shows few signs of abating. Driven by grievances sharpened over decades, the rebels and their supporters demand greater autonomy and political decentralisation. Mediators and external powers should push the warring parties to abide by commitments they have already made to respect a ceasefire. They should then broker a deal to bring the rebels into the national peace process and, later, the constitutional negotiations that this process calls for. The country’s outside partners should also forge grassroots support for a deal in places afflicted by conflict.

Many Equatorians feel that the region has been excluded from negotiations to end the civil war, which helps explain why its conflict has become entrenched. After war broke out in 2013, most Equatorian politicians shied away from involvement, leaving the main belligerents Kiir and Machar to battle it out, although they did ask to be included in peace talks. When Kiir blocked their inclusion as a bloc, armed factions from Equatoria rose up against the national army. Unable to unite, many of them drifted into Machar’s camp, adding tinder to the feud burning between him and Kiir and prolonging the war. Yet as talks focused on finding a deal between Kiir and Machar, Equatorians continued to feel sidelined. In 2017, Thomas Cirillo, a top Equatorian general in the national army, broke off and declared his own insurgency in the region, gaining the loyalty of major opposition commanders south and west of Juba. Although Kiir and Cirillo committed to a ceasefire of their own in early 2020, that agreement quickly broke down. The holdout general’s units today are fighting the forces of both Kiir and Machar.

As long as this insurgency endures, South Sudan is unlikely to be able to consolidate peace, notwithstanding the deal between Kiir and Machar, which is holding for now. Equatoria is a cornerstone of the country. It was the birthplace of the 1960s liberation movement that set South Sudan on the path to independence from Khartoum, and its people have a long tradition of advocating and fighting for autonomy. Today, besides being home to the capital, the region is the gateway to neighbouring countries to the west and south. Its peoples are mixed in ethnicity but have a common aversion to political domination by outsiders. Their relations are particularly bitter with the Dinka, Kiir’s ethnic group (and South Sudan’s largest), who have moved into the region, often with large herds of cattle guarded by heavily armed and abusive militias. Local sympathy for Cirillo’s demands is strong, even as his forces are also accused of mistreating civilians.

International efforts need to ensure that Equatoria is part of the national reconciliation effort. Mediators and external powers should push for Juba and Cirillo to fulfil the terms of their ceasefire deal, including incorporating Cirillo’s representatives in the existing ceasefire-monitoring body. They should also press Kiir to bolster and Cirillo to join the constitution-making process that the deal between Kiir and Machar provides for. This way, the holdout rebel leader will have an avenue to press home his demands at the table, instead of on the battlefield. To complement these top-down efforts, all parties will need to work together to win grassroots support for the deal and to tackle the local grievances against the government and ruling elite that underpin the intense political alienation found across Equatoria.

Map of South Sudan

II. The Roots of Equatorian Political Demands

South Sudan’s brutal civil war beginning in 2013 has been mostly defined by the conflict pitting Kiir, an ethnic Dinka, against his vice president and chief political rival Machar, a Nuer. While the country’s international partners have engaged in relentless diplomacy to bridge this divide, leading to a 2018 peace deal that produced a ceasefire and unity government in 2020, a bloody insurgency simmers in Equatoria, led by Cirillo, whose loyalists are fighting for greater autonomy for the region. Fighting in the area has likely claimed hundreds of lives, if not countless more, since 2016 and forced hundreds of thousands to flee into neighbouring Uganda and the Democratic Republic of Congo (DRC).[fn]Nearly 750,000 South Sudanese fled into Uganda alone in the twelve months after July 2016, when large-scale fighting erupted in Equatoria. Uganda’s entire border with South Sudan is with the Equatoria region. See “Total Refugees from South Sudan – Timegraph” on the Uganda page at the UN High Commissioner for Refugees Operational Portal for South Sudan.Hide Footnote Meanwhile, the political interests of Equatorians, a collection of ethnic minorities, have been largely underweighted in the peace deal, even though the region represents one of the country’s three principal geographical blocs, the other two being Bahr el Ghazal and Greater Upper Nile.[fn]Equatoria borders five countries (the Central African Republic, the DRC, Uganda, Kenya and Ethiopia) and is home to many ethnic groups, including the Azande and Moro in the west, the many Bari-speaking groups of the centre, and the Madi, Acholi, Lotuko and Toposa in the east. At various points in the past century, under both British colonial rule and Khartoum’s, modern South Sudan was governed as three distinct provinces: Bahr el Ghazal, Upper Nile and Equatoria. Because Upper Nile is now also the name of one of South Sudan’s ten states, this briefing will refer to the former Upper Nile province (comprising Unity, Upper Nile and Jonglei states) as Greater Upper Nile.Hide Footnote

Equatoria, the birthplace of southern Sudan’s independence movement, has played a critical role in South Sudan’s rise to nationhood.

These political interests are historical, even if inflamed by recent events. Equatoria, the birthplace of southern Sudan’s independence movement, has played a critical role in South Sudan’s rise to nationhood. Yet Equatorian elites have long felt marginal within the Sudan People’s Liberation Movement (SPLM), which formed in 1983 in resistance to Khartoum’s rule and today is South Sudan’s ruling party. Many Equatorians see the SPLM as a “Dinka” occupying force that has continued to concentrate power in Dinka hands even after liberation.

When it was still part of Sudan, Equatoria was the main theatre for the south’s successive insurgencies against Khartoum. In 1955, on the eve of Sudan’s independence from Britain, Equatorian soldiers raised a mutiny in Torit, the present-day capital of Eastern Equatoria. Next came a series of armed campaigns in the 1960s, eventually coalescing under the Israeli-backed leadership of Joseph Lagu, an ethnic Madi from Eastern Equatoria.[fn]Israel started supplying Lagu’s forces in 1969 with arms, training and military advisers as part of its effort to weaken the Arab nationalist bloc to which the Khartoum government belonged at the time. See Lagu’s account of securing Israeli support in Joseph Lagu, Sudan: Odyssey Through a State: From Ruin to Hope (Khartoum, 2006), pp. 19-215. For an account that includes an Israeli perspective, see Peter Martell, First Raise a Flag (London, 2018), pp. 79-98.Hide Footnote To end the war, Khartoum inked an agreement in 1972 in Addis Ababa that gave southerners ostensible self-rule for the first time with the creation of the semi-autonomous Southern Sudan region.

This first period of quasi-autonomy heralded a new era of ethnic politics, as southerners turned their sights upon one another. By 1980, Lagu and other Equatorian elites were griping that ethnic Dinka, the largest of the South’s many ethnic groups, had poisoned its politics by campaigning on a “Dinka unity” message. They further accused the Dinka of dominating the new southern government’s institutions in Equatoria and its biggest city Juba.[fn]See Crisis Group Africa Report Nº300, Toward a Viable Future for South Sudan, 10 February 2021.Hide Footnote Lagu proposed “decentralising” the South by redividing the area into the three colonial-era provinces of Bahr el Ghazal, Upper Nile and Equatoria. When Sudanese President Jaafar Nimeiri sided with Lagu, thus in effect dissolving the 1972 peace deal, Dinka and other southerners accused Equatorians of undermining the South’s unity.[fn]One South Sudanese chronicler dubbed the intra-South debate of this period “the Unionists vs. the Divisionists”. Arop Madut-Arop, The Genesis of Political Consciousness in South Sudan (2012).Hide Footnote

The animosity between Equatorian and Dinka elites grew even as southerners continued to struggle against Khartoum’s rule. As tens of thousands of southerners fled to Ethiopia amid the escalating unrest and a series of army mutinies, John Garang, a Greater Bor Dinka, formed the SPLM with Addis Ababa’s backing. Although some Equatorians joined the SPLM, especially as time wore on, many rejected the movement as a Dinka force bent on seeking revenge. Many also fled as refugees to neighbouring countries. Others formed anti-SPLM militias that espoused the cause of southern independence even as they received arms from Khartoum. Abuses by the SPLM’s armed wing (the Sudan People’s Liberation Army) against the local population did little to improve its image. Widespread forced recruitment, including of children, deepened Equatorian resentment further.

The fault line between Equatorians and Dinka has remained wide until today. Tensions worsened after independence in 2011, as Kiir monopolised power and South Sudan descended into factional struggles for control of the new state. Equatorians in particular felt under-represented in South Sudan’s powerful security establishment, where Dinka and Nuer dominated the upper ranks. Acrimony over representation in political and security institutions is mirrored by competition over land. In the 1980s and 1990s, large numbers of Dinka resettled in parts of SPLM-held Equatoria, many of whose native inhabitants had fled as refugees to neighbouring Uganda, generating a major new grievance among the Equatorians who later returned. These native residents accuse the Juba government and local security operatives of favouring the Dinka settlers in land and legal disputes.[fn]These resentments are strongest in Nimule, the most important town on the Ugandan border, in the ethnic Madi area of Eastern Equatoria, as well as in Juba.Hide Footnote

Another source of tensions has been heavily armed Dinka cattle herders, many acting as private guards for livestock amassed by Dinka elites, who have moved into Equatoria’s lush lands in recent decades. Equatorians accuse these herders of using their land for grazing without permission, abusing local inhabitants and refusing to compensate farmers for damage to their fields and livelihoods.[fn]Some argue that climate change is a driver of this conflict. See Nhial Tiitmamer, “Resolving climate change-induced migration and conflict in South Sudan”, Africa Portal, 24 May 2020.Hide Footnote While Kiir has, over the years, issued the occasional decree commanding outside cattle herders to leave Equatoria, his orders often go unenforced.[fn]Kiir issued executive orders in 2015 and again in 2017 for herders to return with their cattle to their states of origin. In April 2020, the Equatoria caucus in South Sudan’s national legislature urged Kiir to enforce the orders, deploring the herders’ “bullying, harassment and intimidation”. Press statement, Equatorian MPs, 21 April 2020, copy on file with Crisis Group.Hide Footnote Dinka elites, meanwhile, accuse Equatorians of xenophobia and insensitivity to their kin’s need to make a living.[fn]Crisis Group interviews, 2018-2020.Hide Footnote

Although the Equatorian elites divide their loyalties among South Sudan’s camps, some markers of collective identity and political unity clearly exist. Equatorians’ most consistent political demand has long been federalism or decentralisation. Over the course of the past two decades, Equatorian elites have convened at regional conferences to discuss their most pressing concerns and advocate for redress. These conferences, dating back to 2001 when delegates demanded federal governance, show remarkable continuity and also underscore the longstanding demands that predate the current conflict.[fn]On the 2001 conference, see Adam Branch and Zachariah Cherian Mampilly, “Winning the War, but Losing the Peace? The Dilemma of SPLM/A Civil Administration and the Tasks Ahead”, March 2005. For others, see “First Equatoria Regional Congress: Yei-New Sudan, November 27, 2002 to December 2, 2002”; “Equatoria Conference 2011 – Justice, Unity and Prosperity”, 16 April 2011; “Resolutions, Equatoria Conference 2013: Consolidating Justice, Unity and Prosperity”, 18 February 2013; and “Emergency Equatoria Conference 2014: Resolutions on the Current Crisis in the Country,” 10 January 2014. Copies on file with Crisis Group.Hide Footnote While many Equatorians support Lagu’s old aim of decentralising what is now South Sudan into something akin to a confederacy of three regions, Equatorian politicians recognise that they have not convinced enough non-Equatorians of this agenda to push it forward at this time.[fn]The 1983 division plays a central part in the SPLM’s founding mythology as a supreme betrayal by Khartoum and Lagu. Equatorians remain deeply sensitive to charges from other elites that they have a hidden agenda of separatism rather than southern nationalism. Crisis Group interviews and Crisis Group analyst’s interviews in a previous capacity, Equatorian political, civil and religious actors, 2016-2020.Hide Footnote Instead, most Equatorian elites, including Cirillo, push for greater decentralisation under South Sudan’s federal model, with additional powers and resources devolved to its states and counties.[fn]Cirillo says seeking a confederacy of three regions is a “second option”. Crisis Group WhatsApp interview, Thomas Cirillo, February 2021.Hide Footnote

III. Political Alienation and Snowballing Violence

Even if they believed they ought to have a greater say in the country’s future, Equatorians were reluctant to get involved in the fighting between Kiir and Machar that marked the collapse of the ruling SPLM.[fn]Crisis Group Africa Report N°217, South Sudan: A Civil War by Any Other Name, 10 April 2014.Hide Footnote When civil war kicked off in 2013, Equatorian elites tried to stay neutral in order to insulate their region from the devastating conflict that ensued, and which has now claimed up to 400,000 lives nationwide.[fn]Some of the Equatorian elite considered forming a separate movement, but meetings among the three Equatoria governors in Uganda to lobby for backing from Kampala failed.Hide Footnote This stance captured the popular view among Equatorians that the conflict was nothing but a naked power struggle between Kiir’s Dinka, who predominate in Bahr el Ghazal, and Machar’s Nuer from Greater Upper Nile.[fn]“Governor Konga urges Equatorians to stay out of ‘Dinka-Nuer war’”, Radio Tamazuj, 9 January 2015.Hide Footnote It also reflected the reality that Equatorian elites found themselves divided among differing camps in the factional squabble within the SPLM that pitted Kiir, Machar and other powerful elites against one another, leading to civil war.[fn]Since Equatorians did not have their own contender for the SPLM leadership, the de facto Equatorian political leaders were the governors of the region’s three constituent states – Eastern, Central and Western Equatoria.Hide Footnote

Since that war broke out, Equatorian politicians have steadily pushed – albeit to no avail – for devolution of power by the central government in Juba and for greater autonomy from it. During ceasefire negotiations in 2014, Kiir rejected a bid by the three governors of Western, Central and Eastern Equatoria to form a separate bloc in the peace talks, which would have put them in a position to push for greater self-rule.[fn]Equatorians were prominently represented among the different parties at the peace talks but not as a distinct bloc. See Crisis Group Africa Report Nº236, South Sudan’s South: Conflict in the Equatorias, 25 May 2016.Hide Footnote With no armed group of their own, and lacking external support from the likes of Uganda, which borders the region, Equatorians had scant leverage over Kiir. As a result, disaffected armed elements started drifting into Machar’s camp.[fn]An early attempt by Machar to mobilise Equatorians involved Losuba Wongo and Matata Frank, both now officials in Machar’s camp. Both defected from military administrative positions and travelled to Western Equatoria to train the local Arrow Boys militia. Losuba formed Remnasa, a pan-Equatorian movement that failed to gain a foothold on the ground, before joining with Machar in 2015. He went into exile in the U.S., returning in 2020 as the Machar-appointed minister of federal affairs in Juba. Crisis Group analyst’s interviews in a previous capacity, 2015-2018.Hide Footnote Juba in turn turned up the pressure on Equatorian politicians to remain loyal, actions that presaged the later breakdown into all-out conflict.

Fighting emerged in isolated pockets of the region, as Machar made additional moves to draw prominent Equatorians into his ranks. First, he designated veteran ethnic Bari politician Alfred Ladu Gore as his number two. Then, his rebel movement, the Sudan People’s Liberation Movement/Army – In Opposition, adopted federalism as a demand in a clear bid for Equatorian sympathies.[fn]Crisis Group Report, South Sudan’s South: Conflict in the Equatorias, op. cit.Hide Footnote In Western Equatoria’s Mundri, Wesley Welebe, a former state legislator and local leader of a communal militia, began staging raids on Dinka cattle herders and government soldiers. In Central Equatoria’s Wondoruba, John Kenyi Loburon, a disgruntled police officer, also mobilised to attack the security forces.[fn]Welebe is an ethnic Moro and Kenyi Loburon an ethnic Pojulu. As late as 2015, Welebe publicly denied being in alliance with Machar or waging war against the government. But he swore fealty later. See Alan Boswell, “Conflict in Western Equatoria”, Small Arms Survey, 2016.Hide Footnote As instability ramped up, Machar secured the defection from Juba of Martin Kenyi, a U.S.-educated former Eastern Equatorian militia leader, naming him his deputy military chief of staff.[fn]Martin Kenyi, an ethnic Madi, led the anti-SPLM, pro-independence, Khartoum-backed Equatoria Defence Forces that formed in 1996. These forces sometimes allied with the Khartoum-backed (Nuer-heavy) South Sudan Defence Forces until Kenyi rejoined the SPLM in 2004.Hide Footnote The strategy paid dividends. Welebe and Kenyi Loburon also publicly declared their loyalty to Machar in 2015.

As Kiir and Machar neared their first major peace deal in 2015, Equatorians began to feel locked out of national reconciliation discussions.

Still, as Kiir and Machar neared their first major peace deal in 2015, Equatorians began to feel locked out of national reconciliation discussions.[fn]Crisis Group analyst’s interviews in a previous capacity, 2016. See also Crisis Group Report, South Sudan’s South: Conflict in the Equatorias, op. cit.Hide Footnote Many thought that the peace deal itself was imbalanced. Clauses covering the “conflict-affected states” of Greater Upper Nile, where fighting between Kiir and Machar had raged for two years, granted Machar a share of power in his home region. But the deal offered no such special arrangements for resolving the troubles in Equatoria, even though it was supposed to be a national roadmap out of civil war.

Political friction exploded into violence across much of Equatoria when Kiir and Machar signed the August 2015 deal. Having made concessions to Machar under regional and international pressure, Kiir was keen to suppress demands from another front, in particular Equatoria. Days before signing the peace deal, he sacked Western Equatoria Governor Joseph Bakosoro and Central Equatoria Governor Clement Wani Konga, placing the former in detention.[fn]Bakosoro was held for four days in Juba without charge. He was arrested a second time in December 2015, again without charge, and was not released until April 2016.Hide Footnote In the ensuing power vacuum, two militias in Western Equatoria took up arms against the government, with Alfred Fatuyo, leader of the larger group, the Arrow Boys, declaring loyalty to Machar.[fn]Fatuyo is now the Machar-appointed governor of Western Equatoria. The Arrow Boys were a loose network of community defence vigilantes who became renowned for protecting Equatorians from the brutal Lord’s Resistance Army. They also fought battles with Dinka cattle herders from Bahr el Ghazal, which are not as well known. Fatuyo only partly succeeded in mobilising the network in rebellion. The second militia that rebelled after Bakosoro’s arrest was the South Sudan National Liberation Movement, which refused Machar’s overtures and signed a peace deal with the government in 2016. Boswell, “Conflict in Western Equatoria”, op. cit.Hide Footnote Violence in Western Equatoria spiked, as Kiir’s forces battled those of both Fatuyo and Welebe. Machar also benefited from political realignment: faced with a binary power-sharing deal, with Kiir on one side and Machar on the other, more Equatorians joined the latter.

As the 2015 peace deal took effect, Equatorians aligned with Machar began mobilising in larger numbers across the region under his banner. The recruitment drive took place in all three Equatorian states, including parts of the region that had hitherto been spared conflict, such as Yei, Kajo Keji and Magwi counties, as well as in refugee camps in both the DRC and Uganda.[fn]Yei borders the DRC and Uganda and is primarily home to the ethnic Kakwa. Kajo Keji and Magwi border Uganda; the former is home to ethnic Kuku and the latter ethnic Madi and Acholi.Hide Footnote Many recruits thought they were joining the national army: the peace deal provided for integrating Kiir’s and Machar’s forces. The drive was thus popular because Equatorians thought it would boost their numbers and seniority in the army, which they have long demanded as the equivalents of greater political power. At the same time, commanders used it partly as a tactic to justify their high ranks ahead of the anticipated integration of forces.[fn]Many recruits thought they were joining a peaceful integration process rather than renewed war. Commanders struggled to train or equip these units after war erupted, leading to large-scale desertions. Crisis Group analyst’s interviews in a previous capacity, Equatorian commanders, civil society members and refugees, 2016-2018.Hide Footnote

Kiir chafed at this mobilisation, setting the stage for renewed conflict. He and his generals refused to recognise as a soldier anyone who had not fought government forces. Therefore, they said, Machar’s Equatorian supporters had no place in the army. They sent ill-trained new Dinka recruits (known colloquially as mathiang anyoor) into Equatoria to counter the new threat, stoking local resentment as these forces committed massive human rights abuses against civilians.[fn]Mathiang anyoor, a Dinka phrase, was the name adopted by the (mostly) Dinka recruits from Bahr el Ghazal whom Kiir relied on to defend his regime after the army’s collapse in 2013. By 2016, the cumulative waves of these recruits formed the bulk of Kiir’s fighting force, and his critics began to use the term in a pejorative sense. For more, see Alan Boswell, “Insecure Power and Violence: The Rise and Fall of Paul Malong and the Mathiang Anyoor”, Small Arms Survey, October 2019.Hide Footnote The new Equatorian forces, for their part, started ambushing Dinka travellers on the roads, escalating tensions. In April 2016, when Machar returned to Juba, he promised his Equatorian constituents to take up their demands for inclusion in the army directly with Kiir.[fn]Crisis Group Report, South Sudan’s South: Conflict in the Equatorias, op. cit.Hide Footnote Yet his entreaties yielded nothing but an immediate impasse in the new unity government amid a fresh government counter-insurgency campaign against the Equatorias militias claiming loyalty to Machar, particularly those near Yei.

The peace deal then collapsed, plunging Equatoria into chaos, atrocities and displacement. In July 2016, less than three months after Machar had returned to Juba as first vice president with over a thousand bodyguards, Kiir summoned him to an emergency meeting at the presidential office. While they were meeting, a firefight erupted between their bodyguards, setting off days of battles in the capital. Machar eventually retreated south into the Central Equatorian countryside, linking up with loyal Equatorian commanders – first John Kenyi Loburon, then Wesley Welebe, then Welebe’s deputy Saki Palaoko – who escorted him through the bush for weeks, pursued by government forces, until he and hundreds of starving bodyguards crossed into the DRC’s Garamba Park.[fn]Of these three commanders, only Welebe remains loyal to Machar. Kenyi Loburon and Palaoko both later joined Cirillo. Palaoko resigned from Cirillo’s forces in 2021 and soon afterward was assassinated near Aba, the DRC, in unclear circumstances. Crisis Group WhatsApp correspondence, Equatorians inside and outside the country, February 2021.Hide Footnote Near the border, Machar’s deputy military chief and veteran Equatorian militia leader, Martin Kenyi, whom many Equatorians in Machar’s camp considered their top commander, was left behind and later presumed dead.[fn]For more on Machar’s flight from Equatoria into Congo, see Alan Boswell, “Spreading Fallout: The Collapse of ARCSS and New Conflict along the Equatorias-DRC border”, Small Arms Survey, 2017.Hide Footnote

Equatoria thus became a principal battlefield in South Sudan’s civil war, as Machar’s newly formed armed forces clashed with Kiir’s. The region also descended into a cycle of ethnic killings, with the Machar-aligned forces targeting Dinka and the Kiir-aligned Dinka recruits destroying villages from Yei all the way to the Congolese and Ugandan borders, forcing tens of thousands of civilians to flee.[fn]In 2017, UN satellite images documented rampant destruction of villages, mostly burnt down. The UN counted roughly 10,000 destroyed structures in the vicinity of Yei, and along its major exit roads, and nearly 8,000 more along the road between Kaya and Morobo. “Damage Density Map, Nahr Yei District, South Sudan”, UNITAR, 11 April 2017.Hide Footnote Particularly horrific were accounts of rampant sexual violence against women in Central Equatoria.[fn]Crisis Group analyst’s interviews in a previous capacity, refugees and aid workers, refugee camps and border towns in Uganda and the DRC, 2016-2018. See also Clémence Pinaud, “Genocidal Rape in South Sudan: Organization, Function and Effects”, Human Rights Quarterly, vol. 42, no. 3 (August 2020).Hide Footnote

Despite their key roles in taking on Kiir’s forces, and in saving Machar’s life, Equatorians still felt marginal within the rebel leader’s camp. Machar had never seriously armed Equatorian fighters, leaving them in a mismatch with government forces and unable to defend civilians. Further, Machar often placed the Equatorians under the command of Nuer generals, whom he left behind south of Juba alongside hundreds of his most fiercely loyal and battle-hardened Nuer bodyguards, leading to much Equatorian resentment.[fn]Crisis Group analyst’s interviews in a previous capacity, Equatorian opposition commanders, community leaders and civil society members, 2016-2018.Hide Footnote With Machar in any case exiled in South Africa after his evacuation from the DRC under international duress, and with Kiir under no pressure to welcome him back into the power-sharing government, it looked to many as if the strategy of hitching Equatoria’s wagon to Machar’s star had delivered the region little but devastation.[fn]South Africa held Machar under de facto house arrest after he flew there for medical treatment. Former U.S. officials say Washington was frustrated by the Kiir-Machar power struggle, which it saw as intractable, and wanted to seize the opportunity to push Machar from the picture, even if they were equally vexed by Kiir. Some later admitted it was a mistake to do so. Crisis Group interviews, former U.S. officials, 2018-2019.Hide Footnote

IV. The Birth of an Equatorian Rebellion and the Limits of Mediation

Out of the rubble of Equatoria’s conflict emerged Thomas Cirillo, a top-ranking Equatorian in the military who had once been an important part of South Sudan’s long struggle for independence from Sudan.[fn]In 1992, Cirillo led a high-profile mutiny in Juba, defecting from the Sudanese army to the SPLA, joining the SPLA’s assault on the city from within and becoming one of its major commanders in the area. Cirillo’s defection was especially significant because his older brother Peter Cirillo, a retired Sudanese major general, was the former military governor of Equatoria (1985-1988) and an early founder of the Anyanya rebellions in the 1960s.Hide Footnote In February 2017, he resigned from the national army, his letter accusing the government of “ethnic cleansing” and an array of other crimes, including burning villages, and blasting Kiir for turning the military into a “tribal” outfit that subverted the chain of command and occupied non-Dinka lands on behalf of a “Dinka ruling clique”.[fn]Cirillo’s resignation letter to President Kiir, 11 February 2017, copy on file with Crisis Group.Hide Footnote One month later, with Machar under South African house arrest, Cirillo formed his own movement, the National Salvation Front. Leaving the army without a cohort of troops in tow, he instead relied on defections from Machar’s camp to kick-start his insurgency. Bitter infighting ensued, as those who joined him clashed with those still loyal to Machar.[fn]Such was the fear of losing popular support to Cirillo that the six Machar-appointed Equatorian shadow governors took the extraordinary step of releasing their own press statement welcoming Cirillo’s defection and formation of the National Salvation Front. The shadow governors floated the notion that, if Juba refuses their demand for federalism, Equatorians may need to push for “self-determination” (a position not endorsed by Machar). “Equatorian Governors in the SPLA-IO on Declaration of National Salvation Front of South Sudan”, press release, 9 March 2017.Hide Footnote

Over time, Cirillo wooed a core of militias in parts of Central Equatoria, his home area, and Western Equatoria from Machar to his side. The 2017 defection of Kenyi Loburon, who had been Machar’s top Central Equatoria commander, was especially critical in giving oxygen to Cirillo’s rebellion.[fn]In his declaration of joining Cirillo, Kenyi Loburon stated that Cirillo had been secretly assisting his rebellion while in Juba, complaining as well that Machar had “neglected” his forces. John Kenyi Loburon, “Resignation from SPLM-IO”, 28 July 2017, copy on file with Crisis Group.Hide Footnote But as clashes also continued between the Cirillo and Machar camps, the government retook ground. More civilians fled across the border as refugees. Cirillo and his new commanders relied on a populist Equatorian message to drive supporters away from Machar, but the cost of his rebellion was high, fracturing Equatorians amid additional bloodshed.[fn]Crisis Group analyst’s interviews in a previous capacity, Equatorian opposition commanders in both camps, community leaders and civil society leaders, Uganda, 2017-2018.Hide Footnote Many Equatorian communal leaders began to despair of insurgency.[fn]Crisis Group analyst’s interviews in a previous capacity, Uganda, 2017.Hide Footnote

Cirillo’s emergence rearranged the conflict map by making Equatorians prime actors in the national war for the first time, yet mediators struggled to adjust accordingly. In 2017, when the regional bloc Intergovernmental Authority on Development (IGAD) tried to resuscitate the 2015 accord between Kiir and Machar, they sidelined Cirillo in the talks even though he had become the only significant rebel leader besides Machar. IGAD mediators lumped him together with other groups, known as the South Sudan Opposition Alliance, though none except for Cirillo maintained a major fighting force on the ground nor had much political weight in the conflict.[fn]IGAD backed the Alliance’s inclusion in the talks in part as a response to criticism that the original 2015 peace deal was too narrowly focused on Kiir and Machar. But the group fell into leadership disputes between competing factions. The differences have persisted after the 2018 peace deal, which gave the Alliance the right to one of three vice presidential slots. In 2020, it could not agree on whom to nominate as vice president, so Kiir chose on its behalf.Hide Footnote Cirillo was isolated in the Alliance, which consisted mostly of veteran opposition politicians who considered him a soldier and political neophyte with a provincial agenda.[fn]The Alliance included veteran politicians Lam Akol, Gabriel Chang and Joseph Bakosoro.Hide Footnote

Predictably, Cirillo broke with the Alliance in opposing the peace deal drafts. He argued that the negotiators erred in putting power sharing in Juba over what was really required to bring peace to South Sudan, notably the devolution of authority.[fn]See “Cirillo refuses to sign governance deal without federalism”, Radio Tamazuj, 2 August 2018. Cirillo also chose not to sign amid heavy internal and Western scepticism of the accord. Crisis Group interviews, Thomas Cirillo, 2018-2019. During the talks, the U.S., the UK and Norway – the so-called Troika that has taken the lead (among Western states) on South Sudan diplomacy since 2013 – publicly criticised the emerging Khartoum-brokered peace deal.Hide Footnote He eventually abandoned the peace talks in Khartoum a few months before the new 2018 accord was finished, a fateful decision that led to his eventual rejection of the final deal and the nationwide ceasefire that was supposed to come into effect.[fn]He blamed, in part, Khartoum’s mediation, accusing Sudanese authorities of threatening to deport him and other opposition members to Juba as well as bribing members of his group to sign parts of the peace deal when he refused. Crisis Group interview, Thomas Cirillo, Addis Ababa, 2018. He also made these accusations publicly. “Cirillo says he did not sign peace deal in Khartoum”, Radio Tamazuj, 7 August 2018.Hide Footnote

The costs of failing to preserve Cirillo’s inclusion in talks soon became clear. In the months following the September 2018 deal, even as a ceasefire emerged in the rest of South Sudan, the conflict in Equatoria erupted anew, plunging swathes of the centre and west into combat and civilian displacement. Fighting continued throughout 2019, with Cirillo failing to significantly expand his insurgency and the government failing to stamp it out. In late 2019, with Cirillo continuing to reject the 2018 pact, the lay Catholic Sant’Egidio community started up peace talks in Rome among him, Kiir and others whom the deal excludes.[fn]Sant’Egidio’s first mediation experience came in Mozambique in the 1980s. Since then, the group, founded in 1968 as a social service group aiding the Italian poor, has mediated in Africa, Latin America and the Balkans.Hide Footnote

V. A New Mediation Track

Even Equatorians who do not support Cirillo’s tactics hope that mediation efforts aimed at ending the conflict will culminate in a deal in which, one way or another, Juba finally accepts substantial dispersal of power and resources. The quiet Sant’Egidio negotiations scored a quick success, with the January 2020 Rome Declaration committing the parties to a cessation of hostilities and a renewal of political talks in the future. But mediators suspended a subsequent March meeting as they waited for Kiir to appoint a new unity government delegation to the talks following Machar’s return to Juba in February under the main peace deal.

The COVID-19 pandemic hindered efforts to restart negotiations, especially after the ceasefire between the government and Cirillo broke down in April.

The COVID-19 pandemic also hindered efforts to restart negotiations, especially after the ceasefire between the government and Cirillo broke down in April. Over the subsequent weeks, large-scale government offensives aimed to take back territory held by Cirillo, setting off another wave of civilian displacement.[fn]Amnesty International documented atrocities and widespread destruction in the Yei area during the April-June 2020 fighting. “South Sudan: UN arms embargo must be maintained after surge in violence against civilians in 2020”, Amnesty International, 30 November 2020.Hide Footnote Mediators struggled to bring the groups together to restore the ceasefire, given coronavirus-era travel restrictions and the limits of virtual diplomacy.

The talks restarted in Rome only in October, with parties recommitting to the ceasefire and making progress on political matters. Cirillo broke with his main allies in the opposition alliance, which appeared to allow his camp to negotiate directly with Kiir’s camp for the first time.[fn]Cirillo had formed the loose South Sudan Opposition Movements Alliance in The Hague in 2019 with co-signatories Paul Malong, Kiir’s ex-army chief, and Pagan Amum, a former SPLM secretary general who led the Former Detainees faction that refused to sign the 2018 peace deal. The Alliance was never able to agree on a common platform.Hide Footnote The two sides recommitted to the ceasefire and began negotiating a ten-point declaration of principles, reaching agreement on most. They deadlocked, however, over whether a new constitution should go up for referendum, as Cirillo demands, or be subject to a “constituent assembly”, as Kiir’s team prefers and the 2018 peace deal prescribes.[fn]Draft Declaration of Principles, 12 October 2020, copy on file with Crisis Group. Crisis Group interviews, officials present at the Rome talks, February 2021.Hide Footnote Cirillo fears that any constitution produced through a process dominated by Kiir and Machar appointees, as under the 2018 deal, will be subject to their manipulation.[fn]Crisis Group interviews, Thomas Cirillo and officials present at the Rome talks, February 2021.Hide Footnote Kiir’s allies argue that a referendum is impractical.[fn]Crisis Group interviews, Kiir officials and officials present at the Rome talks, 2021. This government position is widely seen as an attempt to keep control of the constitutional process.Hide Footnote

Talks in December failed to make much headway. While Cirillo’s forces were due to join the implementation and monitoring mechanisms of the main ceasefire, alongside Kiir’s and Machar’s commanders, starting in January 2021, the deadline for them to start to do so passed amid heightened doubts over the rebel general’s ability to convince his field commanders to end hostilities.[fn]Kiir officials and foreign diplomats alike express scepticism that Cirillo can exert sufficient control over his ground forces to enforce a ceasefire. The exact degree of his commanders’ loyalty is a matter of debate. Crisis Group interviews, Kiir officials, diplomats, aid workers, local civil society members, Juba, Nairobi, remote, 2018-2021. Cirillo, meanwhile, claims that he cannot cement the ceasefire until the declaration of principles is final. Crisis Group WhatsApp interview, Thomas Cirillo, February 2021; Crisis Group WhatsApp correspondence, another Cirillo delegate to the Rome talks, January 2021.Hide Footnote

VI. Resolving the Insurgency

Halting violence in Equatoria will require a top-level deal between Kiir and Cirillo, to open the door for a comprehensive solution that can deal with Equatoria’s historical grievances and sense of political exclusion. Getting there will not be easy. Cirillo’s trust has been eroded by the constant hostility between Kiir and Machar, as well as the fact that implementation of their peace deal is drastically behind schedule. Kiir, meanwhile, has thus far demonstrated a mixed commitment to talks with Cirillo and is reluctant to embark on the far-reaching constitutional reforms the rebel commander seeks. Fighting has also continued even after the progress made in Rome. Kiir’s weeks of offensives on several fronts in Central and Western Equatoria in April and May 2020 further convinced Cirillo’s allies that the South Sudanese president cannot be trusted.

That said, both men face heavy pressure to end the holdout rebellion that is marring South Sudan’s attempt to turn the page on its civil war. Cirillo’s forces face difficult prospects on the battlefield, where they are now the sole rebels fighting the government.[fn]Cirillo has made clear that his strategy in declining to sign the 2018 peace deal was premised on his belief that it would fail. Crisis Group interview, Cirillo, Addis Ababa, 2018.Hide Footnote The rebel commander lacks a state ally in East Africa and is unable to provide substantial resources to the fighters on the ground, who mostly rely on local illicit means of financing, such as mining and logging.[fn]Some accuse Cirillo’s ground commanders of focusing primarily on securing mining sites. Crisis Group interviews and Crisis Group analyst’s interviews in a previous capacity, community leaders, civil society leaders, aid workers and researchers, 2016-2021. See also “Final Report of the Panel of Experts on South Sudan Submitted Pursuant to Resolution 2428 (2018)”, UN Panel of Experts on South Sudan, 9 April 2019. Other UN rights investigators concluded: “The ongoing clashes are motivated by, inter alia, territorial disputes, access to lucrative gold mines, illegal taxation, extortion and smuggling, and retaliation”. UN Security Council, S/2019/301, “Report of the Commission on Human Rights in South Sudan”, A/HRC/46/53, 4 February 2021. The UN Commission on Human Rights in South Sudan also documented mass abductions by Cirillo’s fighters in Central Equatoria, among other abuses of civilians.Hide Footnote Kiir also faces risks in letting the insurgency continue. Even if fighting does not directly threaten his rule, it destabilises strategic areas near Juba and could become a stubborn thorn in his side. If Kiir hopes to defeat his chief political rival Machar in elections, he will need to cultivate greater support among Equatorians, a major swing voting bloc. Further, continuing conflict could fuel the very separatist sentiments in Equatoria that Kiir’s circle says they must suppress.

There is a clear path to continued talks. First, as already agreed among the parties, mediators should press for Cirillo’s group to be included in the wider ceasefire mechanisms, created under the 2018 accord, to bolster the weaker Kiir-Cirillo ceasefire and consolidate momentum in the talks. Secondly, the talks should focus primarily on how to bring Cirillo into the hobbled constitutional negotiations already promised under the 2018 accord and on how to reinvigorate those constitutional review efforts. This is important given that Cirillo’s prime demands are not about power sharing in the centre but about a new, substantially decentralised political model for South Sudan.[fn]Crisis Group Report, Toward a Viable Future for South Sudan, op. cit.Hide Footnote In essence, Cirillo would stop fighting in return for assurances the constitutional negotiations would be more credible and offer strong prospects for the decentralising reforms Equatorians want. Regional capitals should support such a separate peace process, rather than stick to their stated position that Cirillo simply sign on to the 2018 accord as it exists.

The path to a final deal is less clear. Cirillo seeks far-reaching decentralisation. He will struggle to achieve that goal immediately, but the idea would attract allies across the political spectrum, given the breadth of support for devolution, should Kiir and Machar allow the peace process to proceed and broaden it to include popular participation.[fn]Ibid.Hide Footnote Cirillo’s proposal seeks to devolve 60 per cent of South Sudan’s income out of Juba, with 20 per cent going to its ten states and 40 per cent to its 79 counties.[fn]“Federalism for a Peaceful and Prosperous South Sudan”, National Salvation Front, 2020.Hide Footnote This position is not so far from proposals put forward in Kiir’s own National Dialogue process, which envisaged devolving 45 per cent of South Sudan’s revenue to a 32-state system, even though Kiir has not endorsed this recommendation himself.[fn]“The National Dialogue Resolutions on Governance and Social Cohesion”, South Sudan National Dialogue, November 2020, copy on file with Crisis Group.Hide Footnote Machar has delegated his own constitutional efforts to Oyet Nathaniel Pierino, a former Juba University lecturer from Eastern Equatoria who is a vocal proponent of federalism.[fn]Crisis Group interviews, Pierino, Juba, 2019-2020.Hide Footnote

An inclusive process, whether through constitutional negotiations or a broader dialogue, could bridge differences through compromise and politicking.

Cirillo is unlikely to ever achieve such broad reforms on his own, but an inclusive process, whether through constitutional negotiations or a broader dialogue, could bridge these differences through compromise and politicking.[fn]Crisis Group Report, Toward a Viable Future for South Sudan, op. cit.Hide Footnote Thus, Cirillo could choose either to negotiate a position for himself in the Juba government or to sit out the unity government from exile, while focusing on the constitutional process and preparing to participate in elections. He would likely refuse to integrate his troops into the national army until the constitutional process was complete, given his deep distrust toward Kiir, but mediators could nonetheless propose mechanisms for keeping the ceasefire in place to prevent greater violence and to at least give constitutional talks the best shot possible.

Any elite-level deal needs to be complemented with a grassroots process that begins to address the grievances that have built up due to Equatorians’ experience of abuse and neglect. If left to fester, these grievances will translate into either more recruitment into armed factions or clashes between Equatorians and non-indigenous ethnic groups, notably the Dinka. Given the local nature of grievances across the large region, the best approach may be to mandate a process that follows up on the National Dialogue with recommendations for each state or county, following further consultation with Equatorian communal leaders, including elders and women, as well as with migrant Dinka. Kiir, Machar and Cirillo should bless this process so that all communities feel free to participate. The disputes run so deep that they will likely require spin-off processes for negotiating Dinka cattle grazing rights and local land use. Local religious and civil society actors will also be needed to continue mediating local ceasefires.

VII. Conclusion

Resolving the insurgency in Equatoria is critical if South Sudan hopes to move on from its horrific conflict. Since the civil war erupted in 2013, mediators have tried to bridge the divide between Kiir and Machar, but this focus has hardly proven a recipe for stability. In the absence of a track where Equatorians could address their historical grievances, armed factions from the region have ended up feeding the conflict between the two principal belligerents, prolonging instability nationwide and helping create the conditions for the birth of an Equatorian rebellion. Kiir’s own National Dialogue process, which concluded in November 2020, acknowledged the special intensity of Equatorian discontent.[fn]“The Equatoria Regional Conference was unique in three respects. Firstly, the delegates were highly educated and well informed on the issues they raised for discussion. Secondly, the Conference was emotionally charged, with people speaking bitterly about the situation in their region and in the country as a whole, mirroring the way people spoke at the Grassroots Consultations, specifically how the state was treating the citizens. Thirdly, delegates focused on critical issues regarding land ownership and land grabbing and contributed much to the debate on federalism. There was also much discussion on … the issue of cattle from other states to Equatoria states”. “Covering Note to the National Dialogue Reports”, Office of the Co-Chairs, National Dialogue Steering Committee, n.d., copy on file with Crisis Group.Hide Footnote A reinvigorated and credible constitutional means of pushing demands for greater autonomy could, if paired with a genuine grassroots process for addressing local grievances, help calm tensions and provide an opening for the country’s elites to forge a political settlement among all South Sudanese. Otherwise, conflicts in Equatoria and elsewhere will continue to ignite – at great cost to an already scarred young nation.

Juba/Nairobi/Brussels, 25 February 2021

Appendix A: Satellite Imagery of Destruction in Yei, Central Equatoria, South Sudan in 2017

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