The fringing reefs in Opunohu Bay and Cook’s Bay in Moorea, French Polynesia are an important component of Moorea’s fringing reef system, as they comprise approximately 20% of the island’s perimeter. The two bays are assumed to have differing benthic communities due to differences in onshore land development and freshwater input, but observational studies of their benthic communities are rarely published. To address this information gap, we conducted a quadrat-based benthic survey to determine important drivers of coral spatial variation throughout the bays. Interestingly, we found that coral taxonomic richness and cover did not significantly vary between bays, and corals only declined at the sites nearest freshwater input. Instead, coral richness was significantly greater when the territorial herbivorous damselfish Stegastes nigricans was present. The majority of the corals we documented were relatively small (88% < 10 cm diameter), thus our results support a positive effect of S. nigricans on young coral diversity. Stegastes nigricans could potentially be creating a refuge inside their territories from scraper herbivores for many non-dominant corals, although other potential mechanisms and the context of these benefits warrant further investigation. We conclude that, on the fringing reefs of Moorea’s two major bays, spatial variation in coral richness is more strongly associated with patches of S. nigricans territories than larger-scale differences in onshore land development and distance from freshwater input.