Radullan Sahiron, also known as Commander Putol, was caught somewhere between the towns of Indanan and Patikul yesterday afternoon.
Police officers, backed by troops, led the raid. Details about his capture were sketchy.
Sulu provincial police chief Senior Superintendent Suaibon Jalad said he was still confirming the report.
Sahiron is one of the most wanted top Abu Sayyaf leaders. The government had offered a P5-million bounty for information leading to his capture.
Sahirons notoriety dates back in the early 1990s when he was allegedly involved in the abduction of two Malaysians and a Singaporean.
He was also involved in the high-profile kidnapping of 21 mostly Malaysian and European tourists from a Malaysian island resort in 2000.
The victims were released after ransom was paid.
The Abu Sayyaf is considered a terrorist organization by the United States. It allegedly has ties with Jemaah Islamiyah, al-Qaedas arm in Southeast Asia.
In February, 13 people and over 100 were wounded in three nearly simultaneous bomb attacks in the cities of Davao, General Santos and Makati. The Abu Sayyaf claimed responsibility.
The bombings were the worst terrorist attacks in the Philippines since the 2004 sinking of a passenger ferry, in which over a hundred were killed.
A bomb believed planted by the Abu Sayyaf started a fire that sank the vessel in Manila Bay.
Security forces are currently hunting several foreign terrorists believed to be members of Jemaah Islamiyah who have reportedly slipped into the country and may be plotting attacks. Roel Pareño