Mesophotic reefs, defined as reefs between 30 m - 150m, have been less investigated than their shallower counterparts. Yet, more protected from human activities and bleaching events, they could be refuge zones allowing the resilience of shallow reefs. However, it is currently unknown if their role as refugia for species diversity also extends to functional diversity and thus potentially ecosystem functioning. Using an extensive video field surveys from Mayotte Island in the Western Indian Ocean, we analyzed how taxonomic diversity and functional diversity of coral reef fishes changed along a depth gradient from 10 to 100 m. We found that shallow and mesophotic reefs host different species, but that these dissimilar assemblages share similar richness combinations of traits values. However, when accounting for biomass of species, it appears that functional structure of assemblages differs along the depth gradient, with, for instance, herbivorous fishes being very scarce in deep reefs while large-bodied carnivorous are more abundant. Therefore, surveys of mesophotic fishes should assess not only species, but also trait composition, abundance and biomass. Overall, our results support the claim that extending marine protected areas to mesophotic reefs is required to maximize the protection of both species and functional diversities to eventually maintain coral reef ecosystem functioning and associated services across the broader seascape.