Global threats to ocean biodiversity have generated a worldwide movement to take actions towards improved conservation and management. Several international targets have recommended the adoption of marine protected areas (MPAs) in national and international waters. While establishing MPAs in international waters has proven to be challenging in most of the world, national governments and the Commission for the Conservation of Marine Living Resources (CCAMLR) have succeeded in adopting multiple MPAs in the Southern Ocean. But are these MPAs representative of Southern Ocean biodiversity and ecosystems? Here we examine the current status of Antarctic MPAs and future outlook, using existing benthic and pelagic bioregionalizations as a proxy for biodiversity. Currently about 9.9% of the Southern Ocean is protected in MPAs, with 3.9% being encompassed by no-take areas. While this is a relatively large proportion of protection when compared to other international waters, current Antarctic MPAs are not representative of all bioregions. Implementing additional protected areas, including those currently under negotiation, would move towards better representation of the Southern Ocean benthic and pelagic regions. Also, this assessment of representativeness was conducted on the basis of broad benthic and pelagic bioregionalizations, which generally use physical environmental data to delineate areas of likely-similar biodiversity. However, there may be variations in species pools and ecosystem structure between (or even within) ocean basins, and at a finer scale, than is reflected in the bioregions. Further analysis is needed, across multiple scales to help resolve where patterns of biodiversity exist and whether they are encompassed within existing and proposed MPAs.