AbstractAimResearch on mesophotic coral ecosystems (MCEs) has increased exponentially in recent decades, and the significance of this ecosystem has been recognised both in terms of biodiversity and distribution. However, this research has mostly focussed on corals and is globally sporadic, with the Indian Ocean remaining largely unexplored and overall MCEs under protected. Hence, baseline data on MCE benthic communities is lacking, but nonetheless essential for developing adequate management strategies. Here, we assess the variation in diversity and community structure of MCEs along the depth gradient and among sites in the Indian Ocean and the environmental parameters that are potentially driving these differences.LocationEgmont Atoll, Chagos Archipelago, central Indian Ocean.Time PeriodPresent.Major Taxa StudiedMarine benthic invertebrates, plants.MethodsUsing a remotely operated vehicle, we collected video transects between 15 and 160 m. We analysed the diversity and composition of benthic communities and used DistLM analysis to determine the environmental drivers of the community structure over the depth gradient and between sites.ResultsWe observed distinct benthic communities along the depth gradient, with a strong community break observed at ~60 m. We also identified a clear zonation of the benthic taxa with depth. This zonation was primarily driven by downward irradiance and temperature, with additional environmental processes playing a minor role in structuring the benthic communities.Main ConclusionsWe show that MCEs in the Chagos Archipelago are distinct communities, and their distribution is driven primarily by irradiance and temperature. Our results highlight the variability in benthic community structure of MCEs, both along the depth gradient and at local geographical scales for the study region. This study showcases the uniqueness of MCEs and will aid in predicting their distribution, potential refugia for shallow reefs, and in developing evidence‐based protection for MCEs, to maintain overall marine biodiversity.