Mesophotic ecosystems have been relatively poorly studied in the Indo-Pacific and in particular within the Coral Triangle region. Here we used a mini-ROV to explore the changes in major benthic groups at two sites (~200 m apart) in the Wakatobi Marine National Park, SE Sulawesi, Indonesia spanning shallow water coral reefs (5 m) to deeper water mesophotic ecosystems (80 m). We found very similar patterns at both sites where coral cover peaked at 15 m, declined rapidly by 30 m, and was virtually absent at 50 m. As coral declined there was a marked increase in sponges, soft corals and other encrusting organisms (including ascidians, bryozoans, tubeworms, gorgonians and molluscs). Importantly, our results differ from most previous studies in other geographic locations where hard corals extend much deeper. It is unclear what drives this difference but it may be related to higher levels of turbidity and therefore reduced light penetration in the Wakatobi compared with other areas, which limits the vertical extent of coral development.