This report provides a critical review of approaches to identify areas of high marine biodiversity and how these can be used to inform the selection of MPAs. Biodiversity area is used here to describe areas of species and habitat diversity. The various measures to quantify marine diversity are critically reviewed (e.g. diversity indices, number of species, number of priority species and taxonomic distinctness). The review highlights the limits of data quality and coverage and considers techniques for effort standardisation and validation (assigning confidence) that are fundamental for interpretation of variable data. Particularly in the pelagic and offshore benthic environments appropriate data are so limited that proxy indicators of diversity are required, since data for directly assessing diversity do not exist. We also review past uses of the term biodiversity hotspots and explore issues involved with employing this approach to UK waters.