The dataset describes the spatial distribution of benthic habitats on the insular shelf south of St. Thomas and St. John, U.S. Virgin Islands. These benthic habitats include: (1) Coral Reef Colonized with Live Coral, (2) Pavement Colonized with Live Coral, (3) Rhodoliths with Macroalgae, (4) Rhodoliths with Macroalgae and Bare Sand, and (5) Bare Sand. These habitats were translated into the Coastal and Marine Ecological Classification Standard (CMECS) scheme. NCCOS developed these spatially resolved maps using environmental predictors, underwater videos/photos and mathematical modeling techniques. The overall thematic accuracy for this map is 85.8% (corrected for proportional bias).