Submarine caves are important biodiversity reservoirs, but there is little information about the biota of marine caves in the Southwestern Atlantic. Here, we describe three submarine cavities and their sponge communities on the Fernando de Noronha Archipelago, Northeast Brazil. The underwater cavities were explored and collections were made through scuba diving from 5 to 18 m depths. Sapata Cave has a wide semi-dark zone near the entrance, a narrow transition zone, and a dark chimney, which is closed at the top. Ilha do Meio Cave is narrower and shallower than Sapata Cave, but has a long passage that leads to two completely dark rooms. Pedras Secas Tunnel has only a semi-dark zone with high water movement. The sponge communities in the semi-dark zones of the three cavities are rich and dominated by the classes Demospongiae and Homoscleromorpha, but Calcarea are also common. The transition zones of both caves are dominated by a desma-bearing sponge, thinly encrusting spirastrellids, and small Homoscleromopha and Calcarea. The dark zone in Ilha do Meio Cave is almost azoic, with only three species. This study has increased the number of sponge species known in submarine cavities on Fernando de Noronha from 29 to 69, highlighting the great richness of the sponge communities in these cryptic environments.