Abstract Evolutionary‐based measures of biodiversity play an increasingly important role in theoretical conservation biology, complementing more traditional methods such as patterns of species richness and endemicity. To date, very few studies have used evolutionary data to assess patterns of biodiversity in the Afrotropical region, particularly for freshwater invertebrate taxa. In the present study, the monophyletic Afrotropical freshwater crab family Potamonautidae was used to investigate how phylogenetic data can be combined with other metrics to help develop conservation plans for regional and species‐based conservation efforts. The Afrotropical freshwater crabs make an exceptional group to demonstrate the utility of a phylogeny‐based approach to conservation, as there have recently been a number of phylogenetic studies on this family, the IUCN Red List conservation status is available for almost every species, and accurate distributional range data are available for all species. The conservation priority of this fauna is assessed in relation to the Afrotropical freshwater ecoregions using three traditional measures of biodiversity and two phylogenetic diversity metrics. The results of Evolutionarily Distinct Globally Endangered and Heightened Evolutionary Distinctiveness and Globally Endangered analyses identify both the freshwater crab species and the areas of high conservation priority in the Afrotropical region.