The Deep Reef Refugia Hypothesis suggests that disturbances decrease with increasing depth, thus, reefs at the mesophotic zone potentially serve as refuges for communities found in shallower areas. This study aimed to evaluate fish diversity at shallow and mesophotic reefs at Parque Nacional Espíritu Santo (PNZMAES) and compare them to determine if deep reefs indeed serve as refuges for shallow communities. During 2021-2022 we conducted five-minute video-transects using remotely operated vehicles to document species richness and abundance at shallow and mesophotic habitats. For the recorded species, six biological traits were compiled (length, mobility, position, gregariousness, diet, and activity period) to estimate four functional indices (number of entities, richness, originality, and divergence) as well as Hill’s numbers for taxonomic and functional indices. Furthermore, monthly water turbidity (Kd490) satellite data products were transformed into a light attenuation coefficient (KdPAR) to locate the mesophotic zone (area between 10 and 0.1% of light penetration). At PNZMAES, the mesophotic zone was identified to extend to 21 m under optimal conditions (high stratification and low primary production), which is shallower compared to what is typically observed in oligotrophic regions. The PERMANOVA revealed significant variations in reef fish composition across spatial (site and zone) and temporal (season and year) dimensions. Additionally, univariate tests of functional richness, originality, and taxonomic Hill’s numbers exhibited significantly higher values in the shallow zone. However, functional divergence and functional Hill’s numbers indicated similarities in fish assemblages. Despite differences in fish taxonomic diversity among zones that could be related to less habitat complexity, environmental variation, and resource availability at deep strata, mesophotic reef fish assemblages presented similar functions. This maintenance of functions at mesophotic reefs suggests connectivity between zones and their potential role as a partial refugia in the face of current and near-future disturbances that could affect shallow zones.