Accounting for genetic diversity and evolutionary processes has long been recognised as an important goal in conservation planning. However, because genetic data are often lacking, surrogate approaches are widely used. Few studies have, however, assessed the capacity of surrogate data, such as higher taxonomic levels (e.g. species distributions) to portray intraspecific genetic diversity. Here, we contrast conservation plans based on traditional species distribution data, with those derived from intraspecific genetic data for a smaller subset of species, both using freshwater fish in northern Australia. We modelled the spatial distribution of 46 species and intraspecific genetic diversity within four common species. We then identified priority areas for conservation using both data sets and evaluated the extent to which solutions obtained from species distribution data portrayed genetic diversity. We found that genetic diversity could be adequately represented within priority areas identified using species distribution data, even at low conservation targets and for species with complex genetic structure. However, this was only true when using the entire fish community (i.e. all 46 species). In contrast, a substantial component of the genetic structure would not be represented in conservation priority areas when using a subset of species. Our results have important implications for the use of surrogates for genetic diversity in conservation planning. Sufficient genetic diversity might be represented in conservation priority areas by including a broad range of species with distributions ranging from common to rare elements in the community in the prioritisation analyses. We recommend focusing on improving accuracy of data on species distributions to reduce uncertainties in conservation recommendations derived from commission and omission errors, to avoid misuse of limited conservation funds and potential failure of conservation practice.