We performed a biological survey in the novel system of sinkhole-like structures (“buracas”) of the Abrolhos Bank, Brazil. We found dissimilar benthic assemblages and higher nutrient concentration, microbial abundance (and activity) and fish abundance inside the buracas than in the surrounding rhodolith beds. Our results support the view that these cup-shaped structures trap and accumulate organic matter, functioning as productivity hotspots in the mid and outer shelf of the central portion of the Abrolhos Bank shelf, where they aggregate biomass of commercially important fishes. This distinctive system is being increasingly pressured by commercial fisheries and needs urgent management measures such as fishing effort control and representation in the network of Marine Protected Areas (MPAS).