This thesis focuses on the investigation of reef communities of the Saint Peter and Saint Paul´s Archipelago (SPSPA) across an euphotic/mesophotic depth gradient. Sampling was performed on shallow and mesophotic areas (0 to 90 m depth) using SCUBA and a Remotely Operated Vehicle (ROV). The present work is composed of four chapters: Chapter 1 deals with the quantitative assessment of reef fish communities, which were divided in three distinct communities associated with different depth strata. Clear shifts in habitat use and in size-frequency distributions were recorded for some species. Abundance of black-corals and depth were the most important factors affecting the structure of fish communities, with a clear association of fish with branching blackcorals in the mesophotic zone. Chapter 2 presents the first detailed qualitative assessment of benthic communities of the SPSPA. The influence of biotic and abiotic variables shaping the structure of the benthic communities was evaluated. A total of 77 benthic taxa belonging to six major functional groups were recorded. Macroalgae was the richest group (41 infrageneric taxa), with 17 new records for the SPSPA. Turf algae were the most abundant group on both shallow and mesophotic reefs. Two distinct communities were detected: a shallow one composed primarily by the zoanthid Palythoa caribaeorum (Duchassaing and Michelotti, 1861), the fleshy alga Caulerpa racemosa (Forsskål) J. Agardh, crustose coralline algae (CCA) and Bryopsis spp., and another deeper community dominated by CCA, bryozoans and scleractinian corals. Abiotic variables were the most important predictors of benthic community structure. Chapter 3 brings information on abundance, distribution size and associated fauna (epibionts) of black-corals. Although two species of black-corals, Tanacetipathes hirta (Gray, 1857) and T. thamnea (Warner, 1981), are known to occur in the SPSPA, they are undistinguishable underwater. Epibiosis, mainly by zoanthids and entanglement by fishing monofilament were important factors negatively affecting the health of blackcoral colonies. Black-corals were intensively used as refuge by reef fish, especially by the endemic oblique butterflyfish Prognathodes obliquus (Chaetodontidae). A single black-coral colony repeatedly visited and monitored for ten years showed a decrease in vitality since the first observation, mainly related to fouling by algal detritus and entanglement by fishing monofilaments. Chapter 4 discusses the ecology (abundance, distribution and habitat preferences) of the fireworm Hermodice carunculata, a major predator on mesophotic zone of SPSPA. A total of 278 individuals of bearded fireworm were observed, with significant difference in abundance between euphotic and mesophotic zones. A direct association of H. carunculata with black-corals (Tanacetipathes spp.), the scleractinian Madracis decactis and depth was found. A final session with concluding remarks wraps up information on the ecology of Mesophotic Reef Ecosystems highlighting their possible importance ...