Until his arrest in 2011, the spiritual leader of JI was the organization's founder and the father of Indonesian Salafi extremism Abu Bakar Bashir. In 1972, he co-founded the Pesantren Al-Mukmin religious school with Abdullah Sungkar, where he preached Salafi Islam and political extremism in the spirit of the Dar al-Islam movement, of which he was a member. Many graduates of that school later joined the ranks of JI, which was created by Abu Bashir in the early 1990s during his exile in Malaysia. He joined the jihad after returning to Indonesia after the fall of the Suharto regime. Abu Bashir was convicted of masterminding the explosion at the Marriott Hotel in Jakarta in 2005, but spent just one-and-a-half years in prison. Upon his release in 2009, he founded a new extremist organization called Jamaah Ansharut Tauhid (JAT)
. He was again indicted of organizing a jihadist military camp in Aceh in 2011. He is currently serving a 15-year sentence, but this has not prevented him from releasing a video from prison pledging his allegiance to the Islamic State.
An influential figure in JI until his arrest in Thailand in 2003 was Riduan Isamuddin, also known as Hambali, who is responsible for carrying out military operations and planning major terrorist attacks. He received his military training in Afghanistan, where he fought on the side of the mujahidin in the 1980s. He acted as a liaison man with al-Qaeda, being its head of operations in East Asia. He was also in charge of distributing funds from al-Qaeda. He is currently a prisoner in Guantanamo.
The majority of JI leaders were either seized or killed by Indonesia's Detachment 88 counter-terror squad. Zarkasih, who was appointed emir of JI after the arrest of Hambali, was arrested in 2007. Its top leaders also included the most wanted terrorists in Southeast Asia: Azahari Husin (killed in a clash with police in 2005) and Noordin Mohammad Top (killed in 2009), who were both originally from Malaysia. Azahari Husin, a British-trained engineer, was the chief explosives expert. Mohammad Top, a former accountant, was behind the 2003–2004 terrorist attacks in Jakarta and the 2005 attacks in Bali. Several former JI leaders, such as Malaysian extremist and Afghan war veteran Nasir Abbas, renounced violence and even started helping the Indonesian and Malaysian authorities track down and arrest terrorists.