Jalil Omar, a Muslim preacher, was seized from his boarding house in Lamitan City, capital of Basilan island before dawn and taken to a nearby mountain area, said police commander Chief Inspector Rolando Dimocrito.
Omar had been a member of the Non-Violence Peace Group, a non-government organisation working for peace with Muslim rebels in the troubled island of Basilan, which has a Muslim majority but also a large Christian population.
It was not known why he was kidnapped. A few of his possessions were taken by the gunmen, police said.
Lamitan City Mayor Roderick Furigay said they have not received reports of any demands for his release.
It was unclear how long Omar had been in the country.
He had chosen to remain in Basilan even after the other members of his group had left, officials said.
It was the latest abduction to rock the southern Philippines in recent months following a rash of kidnappings, including the seizure of three Red Cross workers by Muslim extremists.