Jemaah Islamiyah (JI), the South East Asian terrorist organisation based in Indonesia, remains active and dangerous, despite the mid-August 2003 arrest of Hambali, one of its top operatives.

Though more than 200 men linked or suspected of links to it are now in custody in Indonesia, Malaysia, Singapore, and the Philippines, JI is far from destroyed. Indonesian police and their international counterparts have succeeded in seriously damaging the network, but the bombing of the J.W. Marriott Hotel in Jakarta on 5 August provided clear evidence that the organisation remains capable of planning and executing a major operation in a large urban centre.

The information emerging from the interrogation of JI suspects indicates that this is a bigger organisation than previously thought, with a depth of leadership that gives it a regenerative capacity. It has communication with and has received funding from al-Qaeda, but it is very much independent and takes most, if not all operational decisions locally.

New information suggests that JI was deliberately set up as a military organisation and that the division into units known as mantiqis and wakalahs – originally defined as districts and subdistricts – was actually a territorial command structure of brigades, battalions, companies, platoons, and squads.

All senior members of the central command trained in Afghanistan in the late 1980s and early 1990s, before JI formally existed. It was in the camps of the Saudi-financed Afghan mujahidin leader Abdul Rasul Sayyaf that they developed jihadist fervour, international contacts, and deadly skills.

Afghanistan veterans became the trainers of a new generation of mujahidin when JI set up a camp in Mindanao from 1996 to 2000 in a reciprocal arrangement with the Moro Islamic Liberation Front (MILF). The recruits trained in everything from explosives to sharp-shooting and included not only JI members but also members of like-minded jihadist organisations from other parts of Indonesia, especially South Sulawesi and West Java. This means that Indonesia has to worry about other organisations as well, whose members have equally lethal skills but do not operate under the JI command structure. This background report describes the emergence of one such organisation in South Sulawesi that was responsible for the bombing of a McDonald’s restaurant and a car showroom in Makassar in December 2002.

The JI network is held together not just by ideology and training but also by an intricate network of marriages that at times makes it seems like a giant extended family. Insufficient attention has been paid to the role the women of JI play in cementing the network. In many cases, senior JI leaders arranged the marriages of their subordinates to their own sisters or sisters-in-law to keep the network secure.

JI also depends on a small circle of pesantrens – Muslim boarding schools – to propagate jihadist teachings. Of the more than 14,000 such schools in Indonesia, only a tiny number are committed to jihadist principles, but there is a kind of JI “Ivy League” to which JI members send their own children. Chief among these is Pesantren al-Mukmin, better known as Pondok Ngruki, whose founder, Abu Bakar Ba’asyir, is believed to have been JI’s amir or top leader between late 1999 and 2002.

JI thus remains dangerous. The arrests of Hambali and others surely have weakened its ability to operate, and the Indonesian police and their international counterparts have made major progress in hunting down its members. But this is an organisation spread across a huge archipelago, whose members probably number in the thousands. No single individual is indispensable.

The one piece of good news is that there are some indications that internal dissent is building within JI. Members are said to be unhappy with recent choices of targets, including the Marriott hotel bombing that killed mostly Indonesian workers. There is disagreement about the appropriate focus for jihad and over the use of a practice known as fa’i – robbery of non-Muslims to support Islamic struggle. Internal dissent has destroyed more than one radical group, but in the short term, we are likely to see more JI attacks.

Jakarta/Brussels, 26 August 2003