Khaddafy Janjalani's death was confirmed after DNA tests were conducted in the U.S. to compare tissue samples taken from remains found buried in the jungles of southern Jolo island in December with those of Janjalani's imprisoned brother, military Chief of Staff Gen. Hermogenes Esperon said Saturday.
The news came just days after U.S.-backed Philippine troops killed senior Abu Sayyaf commander Abu Sulaiman, marking a major victory in a U.S.-backed campaign to wipe out Islamic militants in the south of the archipelago after years of bombings and kidnappings.
"The Armed Forces of the Philippines is proud to announce that we have neutralized the center of gravity of terrorism in the Philippines," Esperon said in a news conference.
Esperon said the DNA tests were conducted by the FBI. DNA samples were taken for comparison from Janjalani's brother, Hector, who is serving prison time, he said.
Janjalani, who carried a $5 million bounty on his head offered by Washington, had been arrested but escaped from a detention cell at the national police headquarters in 1995. He took over as Abu Sayyaf chieftain after his elder brother, group founder Abdurajak Abubakar Janjalani, was killed in 1998.
Janjalani was killed in a clash with soldiers on Sept. 4, about a month after the military launched a major offensive there.
U.S.-backed Philippine troops launched "Oplan Ultimatum" on Aug. 1 on Jolo, about 600 miles south of Manila, targeting Janjalani and other Abu Sayyaf leaders, and two top Indonesian terror suspects -- Dulmatin and Umar Patek. Dulmatin and Patek are blamed for the October 2002 Bali, Indonesia, bombings that killed 202 people, and have provided bomb-making training to Indonesian and Filipino Muslim extremists.
The Sept. 4 gunbattle also left six marines dead. Government troops believed they had killed a number of Abu Sayyaf fighters, the military said.
Janjalani and his key commanders have been charged with several deadly attacks in the Philippines, including a 2004 bombing that gutted a ferry, killing 116 people in one of Southeast Asia's worst terrorist strikes.
They also carried out a mass kidnappings, including the seizure of dozens of students and teachers on the southern island province of Basilan in 2000, and abduction of 17 Filipinos and three American tourists -- missionary couple Martin and Gracia Burnham and Guillermo Sobero -- in from a resort island in May 2001.
Sobero was beheaded by the militants and Martin was killed during a military rescue in June 2002 in which his wife was wounded.
Philippine army Special Forces troops and Abu Sayyaf gunmen clashed on Jolo on Tuesday and troops recovered the body of one of the militants, who was confirmed by the military the following day as Abu Sulaiman.
Sulaiman, an engineer whose real name is Jainal Antel Sali Jr., is believed to be one of two possible successors of Janjalani. He also carried a $5 million bounty from Washington.
The deaths of Janjalani and Sulaiman leave Radulan Sahiron, a one-armed commander, Isnilon Hapilon and Abu Pula among the senior Abu Sayyaf veterans still active, along with about 400 followers.