The fighting erupted Tuesday in Patikul town on Jolo Island, 1,000 kilometres south of Manila, killing 14 Abu Sayyaf rebels and one marine, said Lieutenant Colonel Ramon Zagala, a military spokesman.
Brigadier General Martin Pinto, a marine brigade commander, said troops seized the Abu Sayayf camp in Patikul on Monday, after bombarding it with artillery fire.
The camp had about 50 makeshift huts that could accommodate around 100 people and bunkers with individual foxholes, he added.
The Abu Sayyaf has been linked to the international terrorist network al-Qaeda and its regional arm, Jemaah Islamiyah.
The rebels have also been blamed for some of the worst terrorist attacks in the Philippines and high-profile kidnappings of foreign hostages.
They are believed to be currently holding captive two European bird watchers abducted in February 2012 and a Chinese tourist and Filipino resort worker abducted from Malaysia earlier this month.