An international effort is underway to establish a representative system of marine protected areas (MPAs) in the Southern Ocean to help provide for the long-term conservation of marine biodiversity in the region. Critical to this undertaking is understanding the distribution of benthic assemblages. Our aim is to identify the areas where benthic marine assemblages are likely to differ in the Southern Ocean including near-shore Antarctica. We achieve this by using a hierarchical spatial classification of ecoregions, bathomes and environmental types. Ecoregions are defined according to available data on biogeographic patterns and environmental drivers on dispersal. Bathomes are identified according to depth strata defined by known species distributions. Environmental types are uniquely classified according to the geomorphic features found within the bathomes in each ecoregion. We identified 23 ecoregions and nine bathomes. From a set of 30 types of geomorphic features of the seabed, 846 unique environmental types were classified for the Southern Ocean. We applied the environmental types as surrogates of different assemblages of biodiversity to assess the representativeness of MPAs. We found that for existing MPAs no ecoregion has their full range of environmental types represented and 12 ecoregions have no MPAs. Current MPA planning processes, if implemented, will substantially increase the representation of environmental types particularly within 7 ecoregions. To meet internationally agreed conservation goals, additional MPAs will be needed. To assist with this process, we identified 119 locations with spatially restricted environmental types, which should be considered for inclusion in future MPAs.