This dataset contains the percentage cover of the stony corals (Scleractinia) and other major groups analyzed from 0.5 x 0.5 m photographic quadrats at several reef habitats at the Moorea Coral Reef LTER, French Polynesia. This survey has been repeated annually in April since 2005. There are two tables available, providing different views of the same data: a long table having all values in one column and a wide table having a separate column for each observed object. Functional groups counted are: Scleractinian Corals (by genus where appropriate, see methods), Macroalgae, Crustose Coralline Algae / Bare Space, Soft Corals, Hydrocorals (Millepora), Algal Turf and Sand. The coral community was sampled photographically in all represented habitats surrounding the island: Fringing Reef, Lagoon, and Outer Reef. The sampling regime consists of a repeated-measures protocol in each habitat, and is structured by habitat to allow a statistical contrast of sites, shores, times, and in the case of the outer reef, depths. Detailed methods are available in the protocols section.