For six decades Vieques Island was used for US Navy military activities. While several studies have addressed the possible impact on shallow coral reefs, mesophotic reefs (30-100 m deep) have been largely overlooked. This study provides an extensive baseline qualitative and quantitative characterization of Black Jack Reef including variations in the light attenuation coefficients, which serve as a proxy for changes in water quality. Operational limitations due to depth were solved using the Seabed Autonomous Underwater Vehicle (AUV). This AUV specifically designed for benthic surveys, was used to obtain two perpendicular phototransects covering a total of 5km at depths ranging 30-51 m. Mean live coral cover was 32% with Montastraea and Agaricia as the dominant genera. Very low levels of bleaching or diseases were found. Sponges were present in both transects with an average cover of 7-9%. The most common sponges were Amphimedon compressa, Aiolochroia crassa, Agelas, Aplysina and Xestospongia muta. Gorgonians and Black corals were present in very low abundance. Extensive areas of rhodolith beds were found. Turbidity does not appear to be a determinant factor at Black Jack Reef.