A 0.0625 m2 mini-box corer (MBC) was used to study the vertical distribution of macrobenthos in the shallow sublittoral zone of Admiralty Bay, during the 2003/2004 summer, near the Brazilian Station Comandante Ferraz, and the Peruvian Station Machu Picchu. Sediment samples were taken from 20, 30 and 60 m, and stratified for particle-size, total organic matter (TOM) and faunal composition analysis. The most abundant taxa were Polychaeta, Oligochaeta, Amphipoda, Cumacea, Bivalvia and Gastropoda. In general, macrofauna were concentrated in the 0–4 cm layer (64% of total organisms). Correlations between sediment characteristics and faunal densities have not completely explained neither the aggregation of organisms at the surface sediment layers nor the differences in faunal composition between locations at 20 m depth. Analysis of parameters such as organic carbon, heavy metals, interstitial water, and species composition should contribute to a better understanding of the diversity patterns found in this study.