We provide a worked example of how a systematic conservation planning methodology (Margules & Pressey, 2000) might be used to identify important areas for conservation of biodiversity in the pelagic environment, using Subarea 48.2 (South Orkney Islands) as a pilot study area. The aim of the worked example is not to identify areas for protection or management at this stage, but rather to test the utility of this methodology, and to demonstrate the types of data and the range of decisions that would be required to undertake such an analysis. ‘MARXAN’ software (Ball & Possingham, 2000; Game & Grantham, 2008) is used to objectively determine the possible contribution of individual areas towards meeting conservation targets, using example datasets for pelagic species, bioregions and other environmental characteristics. It is concluded that this methodology could be used to provide meaningful results with those datasets currently available. With further refinement, the results from this type of analysis could be used to inform the implementation of a range of actions to conserve marine biodiversity.