Geographic isolation, a relatively low species richness and high endemism make oceanic islands excellent natural laboratories for ecological and evolutionary studies. Here we used Baited Remote Underwater stereo-Video systems (stereo-BRUVS) to investigate the taxonomic, trophic and size structures of fish assemblages from pelagic and mesophotic reef ecosystems in the smallest archipelago of the equatorial Atlantic Ocean, the Saint Peter and Saint Paul’s Archipelago (SPSPA). The occurrence of steep reef walls favors studies on the ecological connections between pelagic and reef ecosystems. We performed five pelagic stereo-BRUVS deployments and fourteen benthic stereo-BRUVS deployments, totaling 1440 min of footage. We recorded 14 species from eight families in the pelagic ecosystem, with Carangidae and Balistidae as the most diverse families. The most abundant species were Elagatis bipinnulata (Quoy and Gaimard, 1825), Melichthys niger (Bloch, 1786), and Caranx crysos (Mitchill, 1815), which together accounted for over 75% of the total relative abundance. The carnivores were the most diverse and abundant trophic group. On the mesophotic reefs, 41 taxa were recorded, with carnivores and planktivores being the most diverse, whereas omnivores were the most abundant. Here, the most abundant species were M. niger, Azurina multileneata, Chromis vanbebberae, Seriola rivoliana, Caranx lugubris and Stegastes sanctipauli. Nine species were recorded in both ecosystems, with Melichthys niger, Caranx lugubris and S. rivoliana being the main species linking them (i.e., occurring in both). These species are known to forage in both pelagic and mesophotic reef ecosystems, and thus represent potential ecological links between them. Such links combined with the endangered status of some species, suggest the need for an integrated management strategy in this remote archipelago.