Prohibition of fishing in a marine protected area (MPA) increases predatory fishes and provides opportunity to examine their top-down effects on lower trophic-level species. By taking into account of habitat (anemone) size, we compared juvenile, adult and total (juvenile + adult) abundance of anemonefishes (Amphiprion frenatus and Amphiprion perideraion) on each habitat between inside and outside a MPA at Laguindingan, the Philippines. Total abundances of both species were significantly lower inside this MPA, while separate analyses on the juvenile and adult abundance detected significant MPA effects only for A. perideraion probably due to low statistical powers. As previous studies showed that biomass of potential predators of anemonefish were more than 3 times greater in this MPA, our results suggest that juveniles and adults of two anemonefishes may be decreased there due to stronger top-down effects. Such lower abundance of anemonefish inside than outside a MPA may be a unique case because anemonefish is often exploited in unprotected areas for the aquarium trade.