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    This dataset provides a map of benthic habitats in the nearshore waters of Puerto Rico. The Biogeography Branch of NOAA/NOS/NCCOS acquired aerial photographs of the nearshore waters of Puerto Rico and the U.S. Virgin Islands in 1999. These images, along with field sampling for validation, were used to create geographic information system (GIS) maps of the study area's coral reefs, seagrass beds, mangrove forests, and other important marine habitats. Mapped areas encompass the insular shelf between the shoreline and shelf edge, except where turbidity prevented visualization of the bottom. NOAA's partners included: Government of the Virgin Islands Department of Planning and Natural Resources (VIDPNR) Commonwealth of Puerto Rico, Department of Natural and Environmental Resources Caribbean Fisheries Management Council National Park Service NOAA, National Geophysical Data Center NOAA, Coastal Services Center NOAA, National Geodetic Survey St. Croix Environmental Association NOAA mapped 21 distinct benthic habitat types within eight zones and added these data to a GIS using visual interpretation of orthorectified aerial photographs. Benthic features mapped covered an area of 1600 km2?in Puerto Rico, including 721 km2?of submerged vegetation, 756 km2?of coral reef and colonized hardbottom, 49 m2?of unconsolidated sediment, and 73 km2?of mangroves. Since 2002, these maps have been used for a wide range of applications, including: coral reef monitoring, marine protected area design, fisheries assessments, and student projects.