Rocas, the only atoll in the South Atlantic, is located 266 km off the northeast Brazilian coast. Spatial patterns in community structure of meiofauna, particularly nematodes, and macrofauna were examined along a transect through the sediment path from windward to leeward of the Rocas Atoll sand flat. Differences in benthic community structure between four zones of the sand flat were found to be significant and related to the major local processes of carbonate-grain transport and sedimentation. Both meiobenthic and macrobenthic assemblages were significantly more diverse and abundant within the sediment inflow zone (the initial part of the detrital path of Rocas sand flat) than in the other zones, where a clear impoverishment of benthic invertebrates occurred. This first study of the benthos of an intertidal sand flat over a reef island in the Atlantic showed that the meiofauna is numerically dominated by the nematodes Metoncholainus sp. 1 (Oncholaimidae) and Epsilonema sp. 1 (Epsilonematidade), whilst the macrofauna is largely dominated by oligochaetes and large Oncholaimidae nematodes. Analysis of the species composition, trophic structure and abundance of both the meiobenthos and the macrobenthos revealed an impoverished community subjected to an intense water-movement disturbance.