Amilhamja Ajijul, alias Alex Alvarez, died at the scene while his father, Asnalul, was dead on arrival at the Quinipot District Hospital.
Asnalul had a bullet wound in the head.
Four other Abu Sayyaf terrorists were arrested during a raid in Sitio Calabasa in Quinipot district at about 3 a.m.
Witnesses said they saw the four arrested suspects blindfolded with their hands tied as troops whisked them away.
The arrested suspects have been placed under tactical interrogation.
Col. Edgardo Gidaya, Task Force Zamboanga commander, said Ajijul was wanted for the bombing of two shopping malls in Zamboanga City in 2002 that claimed several lives, as well as the kidnapping in 2000 of 53 students and teachers at a Roman Catholic school from Basilan.
"This is a big blow to the Abu Sayyaf," he said. "We had received a report that they were planning something this Holy Week."
Ajijul was also the principal suspect in the bombing in 2002 of a restaurant in Zamboanga City that killed a US soldier taking part in counter-terrorist joint military exercises, he added.
Zamboanga City Mayor Celso Lobregat commended the Navy, Army and Task Force Zamboanga for the killing of Ajijul, who carried a $20,000 bounty on his head.
"We commend the authorities that they neutralized Ajijul immediately," he said. "The long arm of the law finally caught up with him."
Ajijul has a standing multiple warrant of arrest in connection with the deadly bombing of the shopping malls and the nearby shrine of Fort Pilar on Oct. 17, 2002.
Five of Ajijul’s suspected accomplices in the bombings were arrested a week later by Criminal Intelligence and Detection Group agents.
Ajijul’s group was also tagged in the bombing of an eatery in Barangay Malagutay, just outside the military training center where a US serviceman and three other civilians were killed and dozens were wounded on Oct. 2, 2002. — With AP, AFP