Authorities said the blast struck the gate of Fort Pilar, an open-air religious shrine, in the second attack in Zamboanga in three days.
Southcom spokesman Lieutenant Colonel Danilo Lucero told press sources that the bomb was placed on a bicycle which was parked near the gate of the shrine. It exploded about 8 p.m. today.
On Thursday, seven people were killed and more than 100 others injured when bombs damaged two shopping malls.
Some 200 U.S. troops are based here on a humanitarian mission in Basilan, a stronghold of the Abu Sayyaf group linked to al-Qaida.