Carbonate banks have been associated with a depth-window of 0 and 70 m in the major oceans of the world. Crustose coralline algae (CCA) are well recognized as the most important carbonate builders in the tropical Southwestern Atlantic continental shelf, forming structural reefs and extensive rhodolith beds. The Brazilian Fernando de Noronha Archipelago (FNA) is surrounded by poorly known insular shelf mesophotic reefs (>30 m depth). In this study, we used a remotely operated vehicle (ROV) and SCUBA diving to survey benthic features at 11 sites on the FNA. We found that rhodolith beds represent the main habitats of insular shelves of the archipelago from 10 to 100 m depth. Six coralline algae species were identified forming the rhodoliths. The mean abundance of rhodoliths ranged from 294 ± 26 (mean ± SE) to 451 ± 30 ind m−2, while the mean diameter varied between 3.4 ± 0.3 and 5.9 ± 0.4 cm and live surface was always greater than 96%. In addition, we observed mounds built by the sand tilefish Malacanthus plumieri (Bloch, 1786) up to 40 m from the bed boundaries suggesting that M. plumieri populations play an important role in the dispersion of rhodoliths across the FNA shelf.