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Benthic habitat maps of the nearshore marine environment of St. John, U.S. Virgin Islands were created by visual interpretation of remotely sensed imagery. The objective of this effort, conducted by NOAA's Center for Coastal Monitoring and Assessment - Biogeography Branch in partnership with the U.S. National Park Service (NPS), was to provide spatially-explicit information on the habitat types, biological cover and live coral cover of St. John's coral reef ecosystem. The data described herein represent accuracy assessment (AA) sites explored by NOAA field scientists to evaluate the thematic accuracy of the benthic habitat maps of St. John. Considering vessel drift during habitat characterization, the entire evaluation period was most accurately represented by a series of GPS points logged at five-second intervals.