Backed by village militias, the marines launched an assault over the weekend after several Abu Sayyaf militants were monitored in their jungle lair near Talipao town on Jolo Island, marine brigade commander Col Jose Cenabre said.
Marine officers involved in the fighting said three militants were killed in a clash and three more died later in military shelling. Six village militias on the side of the marines were wounded.
Marines were clearing the captured Abu Sayyaf encampment of booby traps and searching for homemade bombs and rebel documents.
The United States lists the Abu Sayyaf, which is notorious for kidnappings for ransom, beheadings and bombings, as a terrorist organisation. There are an estimated more than 300 Abu Sayyaf armed fighters who have survived years of US-backed Philippine offensives.