Microbial carbonates (microbialites) occurred in the Holocene coral reefs at Paraoir, the Philippines. These microbialites appeal grayish to buff in color with a stromatolitic to thrombolitic structures, and encrust on corals directly or on a thin layer of calcareous red algae or encrusting foraminifera that covered the corals first. The microbialites only occur in the lower (earlier) parts of the Holocene reef sequence where Heliopora coerulea dominated. No microbial carbonates were observed in the upper (younger) part of the Holocene reefs that is interpreted to grow in water depth shallower than 6 m on the basis of coral community. Samples of microbial carbonate and associated coral were dated by AMS C-14. The results show that the microbialites formed about 10 to 7.5 kyr BP, nearly coeval to or a few hundred years younger than the corals on which the microbialites encrusted. AMS C-14 ages of samples recovered at reef margins are consistent to Th-230 ages of corals associated with the microbialites, but those recovered in the back reef are much older that the previously published Th-230 ages of corals and interpreted to be reworked into the backreef. It is proposed that the microbialites at Paraoir formed in early Holocene on reef slope when the deglacial sea level was rising rapidly. After 7.5 kyr BP when the sea-level rise slowed down and coral reefs caught up with sea level, the condition became favorable to corals prospered in shallow water, and no longer suitable for microbialite formation.