Conservation of the high seas marine environment poses a significant challenge to policy-makers and managers. Marine conservation efforts are often hindered by the lack of data and the difficulties in addressing multiple, and typically conflicting uses. The majority of extant Marine Protected Areas (MPAs) are in coastal or tropical regions within national jurisdiction. Conservation of high seas MPAs has emerged on the international agenda as a critical issue requiring the application of novel approaches, international cooperation and political will. Knowledge and understanding of the marine environment and data on marine biodiversity are all typically limited for the high seas, and the use of surrogates to assist in the identification of areas of high conservation value is one possible mechanism to address and potentially overcome these limitations. Drawing upon a database spanning more than 20 years and containing approximately 140 000 records of seabird sightings at sea, this study assesses the potential use of seabirds as surrogates for marine biodiversity in the Indian sector of the Southern Ocean. At-sea ranges, species diversity and the distributions of endangered species may be appropriate selectors or filters to identify areas with high conservation values. Integrating policy with science provides an appropriate mechanism to identify and prioritise MPAs in the Southern Ocean.