Based on a dataset of 16,991 and 307 morphospecies of polychaete worms collected from 58 epibenthic sledge deployments across the Scotia and Amundsen Seas, we show that the structures of their shelf, deep-shelf and slope communities are composed of distinct polychaete assemblages spanning regions with Bhigh^, Bintermediate^, and Blow^biodi-versity. Depth has been identified as the main factor structuring the polychaete communities in both seas, countering the prevalent notion of extended eurybathy of the Southern Ocean benthos. From an evolutionary perspective, this strong dissimilarity between shelf and slope fauna could be interpreted as evidence for survival in shelf refugias, rather than migration into deeper waters during glacial maxima. The previously unsampled Amundsen Sea is shown to be diverse, harbouring a high level of taxonomic novelty, with many species new to science. The polychaete community of the inner shelf in the Amundsen Sea (Pine Island Bay) has also been shown to be of deep-sea character, likely due to intrusion of the Circumpolar Deep Water onto the shelf. In the Scotia Sea, our data support the notion of relatively high biodiversity of waters around the South Orkney Islands, South Georgia, and Shag Rocks (all recently established as Marine Protected Areas) and depressed diversity in the extreme environment of Southern Thule.