The distribution of benthic habitats for a 1-kilometer (km) x 1-km area around Crocker Reef in the Florida Keys, USA, is based upon underwater digital images of the seafloor collected on June 24 and 25, 2014 (Zawada and others, 2016). The imagery was collected using the U.S. Geological Survey (USGS) shallow Along-Track Reef-Imaging System (sATRIS), a boat-based, pole-mounted sensor package for mapping shallow-water benthic environments. The polygons contained in the shapefile included in this data release, Habitat.shp, represent the four general habitat types found at Crocker Reef: hardbottom, rubble, sand, and seagrass.