Modern Islamic militancy emerged in Indonesia during the late 1940s and the early 1950s. Darul Islam (Abode of Islam), a radical Islamist group whose vision was to establish an Islamic state in Indonesia, revolted in West Java in the 1950s. The rebellion was crushed, and relatively little was heard about Darul Islam style radicalism in Indonesia until the late 1970s. In mid-1977, the Suharto regime arrested 185, many with Darul Islam connections. Two leaders, Abu Bakr Baasyir and Abdullah Sungkar, carried on the aims and mission of Darul Islam. Indeed, many Jemaah Islamiyah (JI) members draw ideological inspiration from those struggles, while contemporary Darul Islam members have cooperated in JI activities. 
Jemaah Islamiyah was officially founded in 1993-94 in Malaysia where Baasyir and Sungkar were in hiding from the Indonesian authorities. The organization’s struggle is primarily concerned with domestic issues in Indonesia. Its principal goal is the establishment of an Islamic government in Jakarta, followed ultimately by the formation of a unified Islamic state in the Southeast Asian region. Shari’ah law was to govern the region. This Caliphate would stretch from southern Thailand, through the Malay Peninsula across the Indonesian archipelago and into the southern Philippines.
With Baasyir as spiritual leader and Sungkar as operations commander, the two were able to indoctrinate young Indonesians and Malaysians who shared their vision and objectives. Important future leaders emerged here, including Riduan Isamuddin, also known as Hambali, who established contacts with the al-Qaeda network while fighting with the mujahideen in Afghanistan in the 1980s. The fall of Suharto in 1998 and Indonesia’s attempt at building a democratic system of government enabled both Baasyir and Sungkar to return to Indonesia. The organization has carried out many terrorist acts since 2000 in pursuit of its goal, which has made JI a threat to the security not only of Indonesia but of the region as a whole.
Jemaah Islamiyah’s terrorist acts in Indonesia have been directed chiefly against symbolic Western targets. These attacks have a two-fold effect, weakening the Indonesian government and the economy, while also conveying a frightening message to prosperous foreigners. Some of the most recent and well-known terrorist acts include the Bali nightclub bombing (October 12, 2002); the Jakarta Marriott Hotel bombing (August 5, 2003); and the Jakarta Australian Embassy bombing (September 9, 2004).
The first of these attacks forced the Indonesian government to acknowledge JI’s existence and the threat it posed to the country and to foreigners within Indonesia. Other JI attacks include the October 2002 bombing of the U.S. Consulate in Denpasar, Bali, and the Philippines Consulate in Menado, North Sulawesi; the April 2003 bombing of the United Nations building and Soekarno-Hatta International Airport, both in Jakarta; and the July 2003 bombing of the Indonesian Parliament compound in Jakarta. JI was also believed responsible for funding bombings of the metro in Manila which killed 27 people and injured 90 on December 30, 2000.
An August 2003 report by the International Crisis Group (ICG) stated that the links between future JI leaders and Arabs who later played leading roles in al-Qaeda, developed in the years 1985-1995. For these JI leaders, the Afghanistan/Pakistan experience was clearly a radicalizing one. For instance, key JI operative Imam Samudra – who, on 10 September 2003, was sentenced to death by judges for his part in masterminding the Bali bombing – was trained in Pakistan.
Around 1991, Abdullah Sungkar and other senior “Afghan alumni” formalized the structure of JI and outlined this in a small book entitled Pedoman Umum Perjuangan al-Jamaah al-Islamiya (General Guidelines for the Jemaah Islamiyah Struggle). According to this book, at the apex of JI’s command structure was an emir. Abdullah Sungkar (and after his death in 1999, Abu Bakr Baasyir), appointed and directed a governing council for the organization. Although the senior leadership of JI is almost entirely composed of Afghan alumni, it is important to note that many of its foot soldiers are simple pesantren (a Javanese word meaning religious boarding school) graduates.
It must be stressed that the vast majority of Indonesia’s 14,000 plus pesantren teach a moderate understanding of Islam. Only five pesantren are closely linked to JI and teach a fundamentalist interpretation of Islam. These are al-Mukmin in Ngruki, Sukohardjo in Solo, al-Muttaquien in Jepara (Central Java), Dar us-Syahadah in Boyolali (Central Java) and al-Islam in Lamongan (East Java).
Al-Mukmin pesantren, one of the biggest schools with 1800 boarders, is believed by many to be an important recruiting ground for Islamic extremists. Its alumni were responsible for the 2002 Bali bombings, the 2003 Jakarta Marriott Hotel bombing and the 2004 suicide bombings at the Australian Embassy in Jakarta. Ali Gufron (alias Mukhlas), Amrozi and Ali Imron all graduated from there. And the alleged head of JI’s military wing, Zulkarnaen, closely linked to the Marriott Hotel bombing, is also a graduate of this school. The principal of the school, Haji Wahyuddi, in an interview with The Bulletin’s Asia correspondent, Eric Ellis, said, “The problem of terrorism is imported from outside, it is not from Indonesia or from this pesantren.” 
Another pesantren, Ihya as-Sunnah in Jogjakarta, Java, while not easily identifiable with Islamic militants, does however have a controversial track record. It is administered by Jaffar Umar Thalib, a veteran of the anti-Soviet jihad in Afghanistan, who became notorious in the late 1990s for leading a jihad in Ambon, scene of fierce Muslim-Christian clashes. It was from this pesantren that Jaffar raised the Laskar Jihad (Army of the Jihad), a militia suspected of having loose links with JI.
The Indonesian government has belatedly taken action to combat the terrorist threat after the Bali bombings. JI’s existence was finally acknowledged by the government in Jakarta, and it subsequently detained Abu Bakr Baasyir in 2003. Baasyir, however, received a mere 30-month imprisonment in March 2005. The judge maintained he was not directly involved in the incident, but knew of the plan and did little to stop it.
Meanwhile Hambali’s arrest in Thailand in August 2003 created a massive void in JI’s operational leadership and coherence and severed JI’s links to many of its international financial contacts. Yet the organization has managed to remain afloat under its new leader, Abu Rusdan. Other important leaders remain at large in Indonesia, Singapore, Malaysia and the Philippines.
In January 2002, the Singapore government announced the arrest of fifteen suspected terrorists. Of those arrested, thirteen were said to be members of JI. The arrest of Ibrahim Maidin, JI’s top leader in Singapore, revealed the extensive and well-coordinated nature of the organization’s regional network. The Singapore government claims that with these arrests the local chapter of JI has been virtually eliminated. Meanwhile, the momentum of Malaysia’s war on militants increased significantly as the country came under strong pressure from the U.S. to investigate the extent of local involvement in international terrorism.
Notwithstanding these trends, the Singapore government has recently warned that JI has expanded its regional network, and is working closely with similar groups in other countries, particularly the Philippines. There were three explosions at crowded shopping malls and transport terminals in Manila and two cities in the south in February; the attacks were claimed by Muslim rebel group Abu Sayyaf, which the authorities believe has received funding from JI.
For many years, the Philippines authorities have been fighting the Moro Islamic Liberation Front (MILF), the largest Muslim rebel group with about 12,000 fighters, in the southern Philippines island of Mindanao. Despite peace negotiations and a cease-fire between the MILF and Manila, guerrillas connected with the group continue to provide training facilities for Islamic militants from other countries. A new element in the re-emergence of Islamic militancy was seen in March when guerrillas from the Free Aceh Movement seized a fully-laden gas tanker near Sumatra, taking the ship’s captain as hostage.
It is encouraging that Indonesia, under its new president, Susilo Bambang Yudhoyono, has started cooperating with Malaysia, Singapore, the Philippines and Australia to combat terrorism in Southeast Asia. After the Bali bombing, Australian Prime Minister John Howard said that Australia would be prepared to launch a pre-emptive strike against terrorists in another country if he had evidence they were about to attack Australia. At the time, his comments drew strong criticism from Southeast Asian regional powers, including Indonesia, the Philippines and Malaysia; but subsequent developments in the region, including close cooperation in hunting down the Bali bombers, as well as JI cells responsible for the bombing of the Marriott Hotel and the Australian Embassy, reinforced the need for closer military and intelligence cooperation.
In regards to allegations that JI has access to the inner sanctums of power in Jakarta, there is no evidence of Indonesian Armed Forces (TNI) involvement with JI, nor is there any evidence of substantial links. JI is opposed to all forms of secular government and is therefore ideologically opposed to working with the Indonesian military. This is not to say that some groups and individuals currently associated with JI have not had past dealings with the TNI.
The best long-term solution for combating the JI and broader Islamic militancy Indonesia is to sever the connections between institutions that breed Islamic militants from the mainstream of Indonesian Islam. These efforts, coupled with the harmonization of counter-terrorism culture and legislation in Indonesia with those of other regional countries, should, in the long-term, ensure a successful containment of the problem posed by JI and similar groups in Southeast Asia.
Sharif Shuja is Research Associate in the Global Terrorism Research Unit at Monash University in Australia.
1. “Indonesia Backgrounder: How the Jemaah Islamiyah terrorist network operates”, International Crisis Group, December 11, 2002.
2. The Bulletin, September 21, 2004, p.20.
3. Available online at