Concerted efforts are being made to understand the current and past processes that have shaped Antarctic biodiversity. However, high rates of new species discoveries, sampling patchiness and bias make estimation of biodiversity there difficult. Antarctic continental shelf benthos is better studied in the Ross, Weddell and Scotia seas, whilst the Amundsen Sea has remained biologically unexplored largely because of severe ice conditions year-round. Here we report results from examination of the first benthic biological samples taken from the Amundsen Sea. We compare relative abundance, taxonomic richness and faunal composition of isopod families, and genera and species within two example families (i.e. Desmosomatidae and Nannoniscidae) from the Amundsen Sea with complementary sampling from the Scotia Sea. Benthic samples were taken from inner and outer Pine Island Bay (eastern Amundsen Sea) sites using an epibenthic sledge at 500 m. Similar samples were also collected from 15 Scotia arc sites at 160- to 500-m depths. The relative abundance of isopods in the Amundsen Sea samples was high and surprisingly less variable than across samples in the Scotia Sea. The abundance structure of isopods at family level was compared across different Antarctic seas. We found that in the Amundsen, Scotia and Ross Seas two families dominated abundance. In contrast, isopod abundance reported in the literature from Weddell Sea samples was much more evenly distributed across families. The Amundsen continental shelf isopod fauna appears to be rich, with 96% of individuals belonging to currently undescribed species. Most of the genera have either been described or found elsewhere, but for many of these genera it is the first time they have been recorded away from the Antarctic continental slope or deep sea. The Amundsen Sea assemblages differed greatly from the Scotia Sea sites in terms of both composition and (species and generic) richness. This was largely due to high consistency between samples compared with the highly variable Scotia Sea samples. Thorough biological analyses implementing well-structured geographic sampling regimes and the application of phylogeographic analyses on a variety of taxa are required to further explore the geographic structure of biodiversity and the evolutionary history of the Amundsen Sea.