Temperate mesophotic ecosystems are generally poorly understood and in South Africa, few studies have analysed imagery from benthic assemblages in this depth range. This study used a remotely operated vehicle (ROV) to survey and describe benthic communities off the Kei River in the Amathole Region of South Africa's Indian Ocean. The CATAMI classification scheme was used to annotate 215 images from 14 sites in the 30–100 m depth range. Multivariate analyses (Cluster and MDS) produced eight benthic communities and nine corresponding environmental variables were investigated as potential drivers of observed patterns in epifauna. LINKTREE analysis identified depth and substratum as the best distinguishing environmental variables and generated three groups that represent rhodolith beds, macroalgal reefs and animal forests. A major depth break was evident at 74 m that separated rhodolith beds and macroalgal reefs into the upper mesophotic and animal forests into the lower mesophotic zones. Information from this study is important for marine spatial planning and management and contributed directly to the delineation and zonation of the Amathole Offshore Marine Protected Area.