Until his death in a gunbattle on September 4, 2006, Janjalani was considered the nominal leader of the group by the Armed Forces of the Philippines. His older brother Khadaffy, the founder of Abu Sayyaf, died in December 1998 in a gun battle with Filipino forces. Khadaffy's death was officially confirmed on January 20, 2007, through DNA analysis of both brother's remains. Both were natives of Isabela City, currently one of the poorest cities of the Philippines. Located on the North-Western part of the island of Basilan, Isabela is also the capital of Basilan province, across the Isabela Channel from the Malamwi Island. But Isabela City is administered under the Zamboanga Peninsula political region north of the island of Basilan, while the rest of the island province of Basilan is now (since 1996) governed as part of the Autonomous Region in Muslim Mindanao (ARMM) to the east.
Consequently, being on the social or political division line, Basilan, Jolo and Sulu have seen some of the fiercest fighting between government troops and the Muslim separatist group Abu Sayyaf through the early 1990s. The Abu Sayyaf primarily operates in the southern Philippines with members traveling to Manila and other provinces in the country. It was reported that Abu Sayyaf had begun expanding into neighbouring Malaysia and Indonesia by the early 1990s.
The Abu Sayyaf is one of the smallest but strongest of the Islamic separatist groups in the Philippines. Some Abu Sayyaf members have studied or worked in Saudi Arabia and developed ties to mujahadeen while fighting and training in the war against the Soviet invasion of Afghanistan.[14] Abu Sayyaf proclaimed themselves as mujahideen and freedom fighters but are not supported by many people in the Philippines including its Muslim clerics.
Abu Sayyaf is estimated to have a membership of 200 with an extended membership of over 2000.[9][15]
The group was originally not thought to receive funding from outside sources, but intelligence reports from the United States, Indonesia and Australia have found intermittent ties to the Indonesian Jemaah Islamiyah terrorist group.[16] The Philippine government considers the Abu Sayyaf as a part of Jemaah Islamiyah and notes that initial funding came from Al-Qaeda through the brother-in-law of Osama bin Laden, Mohammed Jamal Khalifa, through Islamic charities in the region.[17][18][19] Continuing ties to Islamist groups in the Middle East indicate that Al-Qaeda may be continuing support.[15][20][21]