Sahid Yakan was taken in shortly after he stepped out of a passenger ferry at the city wharf from the nearby island of Basilan, an Abu Sayyaf stronghold, police said.
"We are still investigating the suspect," local police spokesman Senior Inspector Antonio Clarito said, after Yakan’s family denied he was a member of the Abu Sayyaf.
Authorities in this southern port city are on high alert for Abu Sayyaf guerrillas seeking refuge in Muslim enclaves here to flee a massive military offensive in Basilan, police said.
Last week, intelligence operatives nabbed an alleged Abu Sayyaf commander trying to enter Zamboanga. The suspect, Merang Abante, had a P1-million bounty on his head and was wanted for his role in the kidnapping and murder of two Americans last year.
The Abu Sayyaf is a small group of Islamic rebels known for deadly kidnapping raids targeting foreigners, Christians, local businessmen and tourists in Mindanao.
It has been linked by both Manila and Washington to Osama bin Laden’s al-Qaeda terror network and was the target of a joint Philippine-US military offensive last year.
US troops are expected to arrive here later this month for another round of counter-terrorism training exercises, officials said.