This dataset contains species occurrences of deep-sea benthic fauna distributed along the Brazilian Continental Margin (BCM). Existing records from published databases accessible online were synthesized to derive the deep-sea benthic diversity of the Brazilian Exclusive Economic Zone (EEZ). Only records that had been identified to species level and that were found between 200 and 5000 m water depth were included in this final, standardised database. Records were mapped in ArcGIS and the here included shapefiles for each phylum are annexed. Two existing biogeographic schemes for the South Atlantic bathyal and abyssal depths (Spalding et al., 2007 and Watling et al., 2013) were tested using the distribution data of benthic species along the BCM. A third biogeographic scheme was tested to assess the relationship between benthic fauna and deep water masses within the Brazilian EEZ. Species occurrences were assigned to the biogeographical units of each biogeographical scheme from which the three occurrences databases (watling, hybrid, water masses), included here, were generated.