Concern about declining trends in coral reef habitats and reef fish stocks in the Florida Keys contributed to the implementation of a network of no-take marine protected areas in 1997. In support of the efforts of the Dry Tortugas National Park and Florida Keys National Marine Sanctuary to implement additional no-take areas in the Tortugas region in 2001, we expanded the scale of our fisheries independent monitoring program for coral reef fishes in the region. To provide a foundation for the habitat-based, stratified random sampling design of the program, we created a digital benthic habitat map of coral reef and hard-bottom habitats in a geographic information system by synthesizing data from bathymetric surveys, side-scan sonar imagery, aerial photogrammetry, existing habitat maps, and in situ visual surveys. Existing habitat maps prior to 1999 were limited to shallow-water (< 20 m depth) soft-sediment, coral reef, and hard-bottom habitats within Dry Tortugas National Park and did not include deeper areas such as the Tortugas Bank, now partially contained within no-take marine protected area boundaries. From diver observations made during the 1999 survey, we developed a classification scheme based on habitat relief and patchiness to describe nine hard-bottom and coral reef habitats encountered from 1-33 m depth. We provide estimates of area by habitat type for no-take marine protected areas in the Tortugas region. Updated information on the spatial distribution and characteristics of benthic habitats will be used to guide future monitoring, assessment, and management activities in the region. Significant data gaps still exist for the western area of the Florida Keys National Marine Sanctuary and are a priority for future research.