ABSTRACT: The swift decline of coral reefs stands out as a significant biodiversity challenge confronting our generation, and Mesophotic Coral Ecosystems (‘MCEs’; reefs between 30 and 150 meters) have been proposed as refuge habitats that may be less affected by climate change and human impacts compared to their shallow counterparts. However, MCEs are often distinct from shallow reefs, and studies assessing how marine biodiversity changes along the depth gradient and what factors can influence marine communities in MCEs are still scarce. Here, we conducted underwater visual censuses using mixed-gas closed-circuit rebreathers to evaluate how fish assemblages change among islands and environmental characteristics across the shallow to mesophotic depth gradient within the Cabo Verde Archipelago. Our results show that the beta diversity of reef fish assemblages was mainly driven by depth and other environmental variables. A consistent trend of increasing beta diversity from the shallow to the lower mesophotic zone was observed among the islands, with the lowest variation in species composition observed between the shallow (5 to 30 m) and upper (31 to 60 m) mesophotic depths. Lower species richness and higher turnover was observed within lower MCE (61 to 85 m), suggesting saturation in fish richness at small scales, possibly a result of changes in microhabitat heterogeneity. Furthermore, the effect of geography was negligible, and local-scale environment characteristics were the main drivers of differences in species assemblages. Evidence suggests that increased fishing pressure on the most populated island may reduce the biogeographic influence on fish assemblages across the archipelago.