The deep-sea (200–1000 m) seafloor off the southeastern U.S. has a variety of extensive deep-sea coral ecosystem (DSCE) habitats including: deep-water coral mounds; various hard-bottom habitats off Florida including the Miami Terrace, Pourtalès Terrace, and deep-water canyons (Agassiz and Tortugas Valleys); and deep island slopes off western Bahamas and northern Cuba. The dominant structure-forming scleractinian corals are Lophelia pertusa and Enallopsammia profunda; other structure-forming taxa include stylasterid corals, gorgonians, black corals, and sponges. This biota is associated with hard-bottom seafloor of variable high-relief topography which can be remotely identified from bathymetric data. NOAA bathymetric contour maps and digital elevation models were used to identify and delineate the areal extent of potential DSCE habitat in the region from northeastern Florida through the Straits of Florida. These were ground-truthed with 241 dives with submersibles and remotely operated vehicles which confirmed deep-sea coral habitat. We estimate a total of 39,910 km² of DSCE habitat in this region. By comparison, the estimated areal extent of shallow-water coral habitat for all U.S. waters is 36,813 km². Bottom trawling remains the greatest threat to DSCEs worldwide, and as a result NOAA has established five deep-water Coral Habitat Areas of Particular Concern (CHAPCs), encompassing 62,714 km² from North Carolina to south Florida, which will protect much of the known deep-sea coral habitat in this region. High-resolution surveys are not only critical to define DSCE habitats but also to define areas devoid of coral and sponge habitats that may allow for potential bottom fisheries and energy development.