The composition of sessile benthic megafauna communities on mesophotic coral reefs (50 to 65 m depth) was investigated at 3 sites (Noggin Pass, Viper Reef and Hydrographers Passage) over 500 km of the Great Barrier Reef (GBR) shelf-edge, Australia. High-resolution stereo imagery was collected in 4 separate autonomous underwater vehicle (AUV) surveys and used to characterise the substratum and megafauna at each site (2 surveys from Viper Reef, and one from each of Noggin Pass and Hydrographers Passage). Random sampling of 100 images from a 100 × 100 m area at each site indicated that non-reef habitats predominated and that megafauna were largely confined to reef habitats, while a more detailed investigation of these reef substrata revealed diverse benthic megafaunal communities that varied significantly both within and between study sites. There were consistent patterns in the functional ecological groups occupying particular finer-scale habitat types, with phototrophic taxa dominating the flatter tops of submerged reefs and heterotrophic suspensionfeeders occupying steeper habitats. Slope angle, water clarity and productivity best explained the distribution of megafauna on reef habitats. Reduced photosynthetically active radiation (PAR) likely excludes most phototrophic taxa from steeper slopes. These results suggest that the extensive submerged reefs on the outer-shelf of the GBR harbour diverse mesophotic reef communities. Given these results, GBR mesophotic coral ecosystems deserve further study, not only of their benthic megafauna but also their fish and mobile invertebrate communities.