Rocas Atoll is the only atoll in the South Atlantic and one of the smallest atolls in the world, and is mainly built by coralline algae. Even being unique in the world, reefs from its mesophotic zone (i.e., >30 m depth) have never been described. For the first time, we surveyed the bottom features of Rocas Atoll mesophotic zone by using side scan sonar, a remotely operated vehicle and TRIMIX diving. Rhodolith beds were the main habitat observed, composed mainly by crustose coralline algae, and presenting different patterns of bed structure. In deeper areas (60–80 m), most rhodoliths were coalesced in patches of ∼1 m2, while in the shallow areas (20–50 m), the more typical pattern of free-living rhodoliths predominated. Depths between 50 and 65 m were marked as transitional zones in which a step-shaped carbonate reefs were discovered. In addition to describing the rhodolith beds and the formation of carbonate reefs by the coalescence of rhodoliths, we highlight the importance of oceanic areas such as the one investigated here. They are excellent models for testing and understanding the influence of rhodolith beds in supporting the marine biodiversity and in promoting demographic connectivity between shallow and mesophotic reefs.