 JI is considered dangerous despite the arrest of many members |
JI has links to al-Qaeda and has a long track record of bomb attacks in Indonesia.
The most deadly were the near simultaneous blasts in two Balinese nightclubs on 12 October 2002, which killed 202 people, including 88 Australians.
JI has also been implicated in attacks against Christian targets in eastern Indonesia, a suicide bombing outside the Australian embassy in Jakarta in September 2004 and a similar strike at the JW Marriott hotel, also in Jakarta, in August 2003.
But the group was thought to be in disarray following the deaths or imprisonment of many of its senior leaders.
There was also evidence of a split at the top of JI, with some leaders opposing the use of violence.
Some young hardliners, however, remained both willing and able to use deadly force to promote their agenda, say analysts.
And security analysts warned recently that the risk of a repeat of a Bali-style bombings was increasing with the release of dozens of members of the group from prison who were believed to be joining up with the hardliners.
JI's goals
JI is said to have been formed in Malaysia in the late 1980s, by a handful of exiled Indonesian extremists.
The network grew to include cells across the Indonesian archipelago, Malaysia, the Philippines, Singapore and Thailand. Smaller cells might also exist in elsewhere in the region.
Its goal is the establishment of an Islamic state in Indonesia and in other parts of South East Asia. In its formative years JI advocated using largely peaceful means to pursue these goals, but in the mid-1990s the group took on a more violent edge.
 The two Bali bombs killed 202 people, mostly foreign tourists |
This growing militancy was nurtured in part through contacts between JI figures, and senior al-Qaeda personnel then in Afghanistan, says David Wright-Neville of Monash University in Melbourne, Australia.
Under the influence of the latter, JI embraced the idea that its goals could only be secured through a "holy war".
A growing number of JI members became unhappy at the disproportionately large number of unintended Muslim victims of the bombing campaign.
Indonesian security analysts report that the organisation split into two broad factions - bombers and proselytisers. The latter are attempting to steer the organisation towards using preaching as its main weapon.
Adding to these internal divisions has been the sustained pressure applied to JI by Indonesian counter-terrorism agencies, often in concert with counterparts from further afield, notably the US, Australia and other South East Asian states.
This pressure has led to more than 200 arrests of suspected JI members across the region.
JI's alleged spiritual leader, Abu Bakar Ba'asyir, was imprisoned on minor charges stemming from the Bali attacks in 2002, but later acquitted.
The capture of logistics chief Riduan Isamuddin, also known as Hambali, arrested in Thailand and now in US custody in Guantanamo, and the death of a senior bomb maker, Fathur Rahman al Ghozi, killed in a shoot-out with police in the Philippines, have been important.
The death of bomb-making expert Azahari bin Husin, shot dead during a police raid on a terrorist safehouse on Java island, also struck JI a blow.
Operational resilience
But a number of key figures with the logistic and technical expertise required to sustain a level of deadly violence remain at large.
Of particular interest to the authorities is Malaysian JI member Noordin Mohamed Top - whom Australian forensic experts have implicated in both the 2003 Marriott and the 2004 Australian embassy attacks.
 The Bali bombers said they were keen to be "martyrs" |
South East Asian intelligence sources say that former accountant Noordin Top has come to play an increasingly important role within the organisation, filling the operational and logistic vacuum left by those who have eschewed violence, and the arrests or deaths of others.
The militant factions are now looking outside JI for bombers, as the pool of potential attackers shrinks.
Security analysts International Crisis Group warned in May that extremists have the potential to turn non-violent activists into militants.
There are several reasons for JI's durability, one of which is its ability to tap into a general feeling that South East Asian Muslims are victims of a larger anti-Islamic conspiracy led by the US and supported by allies such as the UK and Australia.
Al-Qaeda links
There is still little credible evidence to support the claim that the JI is al-Qaeda's "South East Asian wing", says Mr Wright-Neville, despite links between senior JI operatives and al-Qaeda stretching back about 15 years.
It was the simultaneous presence at al-Qaeda camps in Afghanistan by militants from across South East Asia that facilitated many of the personal relationships that exist between JI and members of other violent South East Asian Islamist groups.
These include the Moro Islamic Liberation Front, a secessionist movement fighting for a Muslim homeland in the southern Philippines, as well as several other Indonesian, Malaysian and Thai groups.
But the weight of evidence suggests that although some JI personnel might be inspired by the larger global mystique of figures such as Osama bin Laden, the South East Asian group remains operationally and organisationally distinct, Mr Wright-Neville says.
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