The head of the armed forces, Hermogenes Esperon, said DNA tests in the United States prove that a body found on Jolo Island was that of Khaddafi Janjalani.
"The FBI test, which was witnessed by three officers from the (state) crime lab, states that the cadaver recovered last December 27 is that of Khaddafy Janjalani, the acknowledged leader of the Abu Sayyaf group," he said.
Janjalani is believed to have died in a clash with Philippine troops in Jolo in September.
He was on the United States' most wanted list of terrorists and the a $5 million reward was offered for information leading to his capture.
Today's announcement comes just days after the military said U.S.-backed Philippine troops had killed another Abu Sayyaf leader, Abu Sulaiman.
The Abu Sayyaf group, which has reportedly received funding from Al-Qaeda, is blamed for the country's worst bombings and mass kidnappings of foreigners and Christians.
(compiled from agency reports)