Philippine troops were tracking the movements of Abu Sayaff leader Albader Parad on the island of Jolo after tip offs from locals.
They caught up with the militant leader early on Sunday at the foot of Mount Tucay.
Parad and five of his colleagues were killed in a gun battle that followed.
One soldier was killed and two were wounded in the exchange.
The army says Parad was running Abu Sayyaf’s day-to-day operations on Jolo.
He was the leader of Islamic rebels who kidnapped three members of the International Committee of the Red Cross on Jolo in January 2009.