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The largely unexplored diversity in temperate mesophotic ecosystems (TME, ~30–150 m depth) has attracted much attention over the past years. However, the number of studies and knowledge of TME diversity and ecology remains limited and geographically restricted. The absence of information on how assemblages vary across environmental gradients and with depth for most regions also limits our capacity to delimit conservation areas and devise management plans effectively. This study focuses on TME from central Chile and describes the depth distribution of reef fishes and benthic invertebrates and algae for the first time. Through the analysis of towed underwater video surveys between 4.7–95.5 m in multiple sites, we show that total reef fish density and richness decrease with depth but increase with local topographic complexity. The depth-related density varies among fish species and trophic groups, and it reverses in the case of Sebastes oculatus, which increases in density with depth. Sponges and gorgonians dominate benthic assemblages below 20 m depth, and brachiopods and anemones increase below 40 and 60 m, respectively. Some of these species form animal forests which, to some extent, replace the shallow-water kelp forests as structural habitat providers. Nevertheless, the reef fish and benthic community do not show a clear structure with depth or across studied sites. We highlight the urgency to intensify and expand the quantitative characterization of these communities, through this and other methodologies, to better define ecological patterns and advance towards conservation plans for TME, including the Souteastern Pacific region.