Alhabsy Misaya, blamed for the abductions of dozens of Indonesian, Vietnamese and Malaysian nationals, was killed in a clash with marines late on Friday in the jungle between the towns of Indanan and Parang in Sulu province.
His body was identified by military officials and captured Abu Sayyaf militants, General Eduardo Ano told The Associated Press.
"We consider him the most notorious kidnapper from that bandit group and this is a big setback to the Abu Sayyaf," Ano said.
Lieutenant General Carlito Galvez of the Western Mindanao Command confirmed the news with Canadian public broadcaster CBC.
Misaya was believed to be holding several abducted Vietnamese sailors in Sulu's jungles, but the hostages were apparently not with him during the clash.
The Philippine military has been undertaking a major offensive against the Abu Sayyaf, a Jihadist terror group that has been based around the Jolo and Basilan islands in the southwestern part of the Philippines for more than four decades and is notorious for bombings, ransom kidnappings and beheadings.
It is blacklisted as a terrorist organization by the US and the Philippines.
Misaya's execution follows the recent death of Muamar Askali, the Abu Sayyaf spokesperson who sailed from Sulu to Bohol to get more hostages from the tourist destination.
Security officials say Abu Sayyaf is still holding about 20 hostages, including 12 Vietnamese, seven Indonesians and a Dutch citizen kidnapped in 2012.
jbh/jlw (AP, dpa)