This study utilized ROV photograph transects to quantify benthic habitat and coral communities among the five habitat types (algal nodule, coralline algal reefs, deep reefs and soft bottom) identified in the Flower Garden Banks National Marine Sanctuary (FGBNMS). ROV surveys were conducted in the mid and lower mesophotic zone of the sanctuary (17-150 m) on both the East Bank and the West Bank. The FGBNMS represents the northernmost tropical western Atlantic coral reef on the continental shelf and support the most highly developed offshore hard bank community in the region. The complexity of habitats supports a diverse assemblage of organisms including approximately 250 species of fish, 23 species of coral, and 80 species of algae in addition to large sponge communities. Understanding and monitoring these resources is critical to both sanctuary inventory and management activities. During the course of the sanctuary's management plan review process, the impact of fishing was identified as a priority issue, and the concept of a research only area was suggested. The purpose of this project is to provide baseline data for all benthic habitats and coral communities.