Alnajar Tampakan was apprehended on Saturday in Zamboanga City following surveillance operations, army spokesman Lt. Col. Joselito Kakilala said.
The suspect was apparently left behind by Kaddafy Janjalanis group when they fled to the main southern island of Mindanao after eluding pursuing troops near the Zamboanga peninsula early this month.
Initial investigation showed that Tampakan took part in the kidnapping of more than 50 children and teachers from a Catholic school in Basilan in 2000.
He is also implicated in the kidnappings last year of four Indonesian seamen and four Christian preachers from the Jehovahs Witness sect. One of the Indonesians died in captivity, while all the rest escaped or were freed after the government launched a massive military operation.
The Abu Sayyaf, a small group of self-styled guerrilla kidnappers, is considered a foreign terrorist organization with alleged ties to the al-Qaeda network by both Washington and Manila.
It has also been blamed for the killing of two American hostages in the past two years. AFP