Despite several works that have documented patterns of diversity in deep sea organisms, trends of diversity and the processes responsible for such trends still remain unclear. To date very few studies have documented the effects of variables such as latitude and longitude in deep-sea organisms in the Antarctic region. We explored the spatial patterns of diversity of benthic gastropods and bivalves in an extensive region about 2200 km long and 500 km wide from the South Shetland Islands to the Bellingshausen Sea in West Antarctica. A total of 134 species from 54 sites was recorded. Alpha diversity and beta diversity (measured as Whittaker’s and Bray-Curtis similarity indices) were highly variable among areas. None of the species richness estimators measured as Sobs, Chao2, Jacknife1 and Jacknife2, stabilized towards asymptotic values in any area. The number of rare species was large with almost half of species represented by 1 or 2 individuals (41%) and most species (62%) restricted to 1 or 2 sites. The partial Mantel test revealed that similarity between sites increased with the decrease of depth differences, but not with horizontal separation.