Brig. Gen. Agustin Dema-ala, head of the anti-terror Task Force Comet, said witnesses had identified the Abu Sayyaf member as having shot dead photojournalist Gene Boyd Lumawag last Friday.
Lumawag, 26, was the photo editor of the independent news agency MindaNews based in Davao City.
"The witnesses know who the killer is and based on (their) description, we know this (man). He is a member of the Abu Sayyaf," Dema-ala said.
Dema-ala said he did not know the motive for Lumawags killing. Probers, however, said he could have been mistaken as an intelligence agent.
Lumawag was shot in the head with a caliber .45 handgun while he was on his way to take a picture of the sunset from the Jolo pier, said Carolyn Arguillas, chairman of MindaNews who was also in Jolo.
In a statement, Arguillas, who was in her hotel room at the time, said she was told by Army investigators they suspected an "urban terrorist group" of the Abu Sayyaf, which is active in Sulu.
"Gene Boyd was looking forward to his first coverage of Eid-al Fitr, the celebration marking the end of the (Muslim) holy month of Ramadan," she said.
Amy Cabusao, a board member of MindaNews, said Arguillas and Lumawag were in Jolo to interview officials as part of a video documentary project on transparency, accountability and governance in the region for the Asia Foundation, a US-based non-governmental group which seeks to foster development in the Asia-Pacific region.
Cabusao said Arguillas and Lumanag received no threats from any group during their stay.
Silvestre Afable Jr., presidential communications director, condemned Lumawags killing. "This is a dastardly act against a journalist doing his job for the truth," he said.
Lumawags remains were flown in to Davao City yesterday afternoon on board a military Nomad aircraft.
Lumawags father, Renato, photo editor of SunStar Davao, said his sons death was "totally senseless."
His elder sister, Dimple, said, "They may have taken the body of my brother but they can never break his spirit. I dont even expect justice here on Earth for my brothers death anymore. I leave it all to God and God alone."
Last month, radio commentator Eldy Sablas, also known as Eldy Gabinales, a vocal critic of the illegal drug trade and illegal gambling, was shot in Tandag, Surigao del Sur. No suspect has been arrested.
The National Union of Journalists of the Philippines said 2004 "is the worst year for Filipino journalists."
The Center for Media Freedom and Responsibility said Lumawag would be the 48th journalist killed since democracy was restored in 1986 and the ninth slain this year. With Edith Regalado, Marichu Villanueva, Artemio Dumlao and wire reports