The South Orkney Islands Southern Shelf (SOISS) Marine Protected Area (MPA) was the first MPA to be designated entirely within the high seas and is managed under the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR). To assist with research and monitoring of the MPA, an international expedition (‘SO-AntEco’) was undertaken in the austral summer of 2016 to contribute towards a better understanding of selected benthic habitats within the region. The benthic assemblages of the SOISS MPA region were found to be strongly correlated with the texture of the seafloor, where hard substrates hosted a greater number of individuals, taxa and biomass with a dominance of filter feeding vulnerable marine ecosystem (VME) taxa, and soft sediments were dominated mostly by deposit feeders. Substantial differences in the abundance of VME taxa were found between sampling gears (shallow underwater camera system and Agassiz trawl). We conclude that camera systems may be more suitable for VME assessments, but additional trawling is advisable for collecting all faunal types and for higher taxonomic resolution. The designation of VME locations based purely on large scale geomorphic classification is not advisable, due to small scale variation in substrate and other local physical influences.