Systematic conservation planning for developing marine spatial protection includes analysis of the spatial distribution of fishing activities, existing management and ecological characteristics. This paper assesses the overlap between habitat (bioregion), existing spatial management and Antarctic krill catch in the Southern Ocean. The analysis required standardised information on the location and extent of spatial fisheries management measures, which was delivered through a Geographic Information System (GIS). During the 2010/11 season, 64% of the CAMLR Convention Area was open to fishing for at least one species. There were important differences between pelagic bioregions in terms of the fraction that was open to fishing, and the distribution of catch within the open fraction. For example, only 26% of the total area open to krill fishing has ever been fished, and this fishing is concentrated in three of the seven bioregions found in the open area. Information on the distribution of catches and catch limits among different bioregions could be used to prioritise protection for bioregions that are currently under-represented in marine protected areas (MPAs). However, conservation planning should take account of uncertainties that result from the different spatial resolution of datasets and the use of long-term averages to identify spatial boundaries.