The World Summit on Sustainable Development implementation plan requires, by 2012, a representative system of marine protected areas (RSMPA) for the purposes of long-term conservation of marine biodiversity. A great challenge for meeting this goal, particularly in data-poor regions, is to avoid inadvertant failure while giving science the time and resources to provide better knowledge. A staged process is needed for identifying areas in data-poor regions that would enable the objectives to be achieved in the long term. We elaborate a procedure that would satisfy the first stage of identifying a RSMPA, including areas suitable as climate change refugia and as reference areas for monitoring change without direct interference of human activities. The procedure is based on the principles of systematic conservation planning. The first step involves the identification of ecologically-separated provinces along with the physical heterogeneity of habitats within those provinces. Ecological theory is then used to identify the scale and placement of MPAs, aiming to be the minimum spatial requirements that would satisfy the principles for a representative system: comprehensiveness, adequacy and representativeness (CAR). We apply the procedure to eastern Antarctica, a region with spatially-restricted sampling of most biota. We use widely available satellite and model data to identify a number of large areas that are likely to encompass important areas for inclusion in a RSMPA. Three large areas are identified for their pelagic and benthic values as well as their suitability as climate change refugia and reference areas. Four other areas are identified specifically for their benthic values. These areas would need to be managed to maintain these values but we would expect them to be refined over time as more knowledge becomes available on the specific location and spatial extent of those values.