1. The rapid degradation of freshwater habitats in southern South America may cause the extinction of the endemic species of Aegla, as well as other freshwater species and components of riverside environments related to them. Information on the distribution of species and their conservation status is essential for developing conservation strategies.2. The updated distribution of Aegla in its southernmost distribution was analysed in order to prioritize freshwater ecoregions, applying biogeographical, phylogenetic and conservation status and complementarity approaches. 3. The distributions of the species of Aegla were delineated on maps and plotted against freshwater ecoregions. A data matrix of areas versus species was constructed and a taxon-area cladogram was created. Ecoregions were ranked, based on their species richness and using a complementarity criterion, to create a list of those considered important for conservation. The conservation status of Aegla species was assessed on the basis of the categories and criteria of the International Union for Conservation of Nature (IUCN) to produce a decreasing order of the risk of species extinction. These assessments were combined to define a consensus ranking of the priority areas for conservation. 4. The areas of maximum species richness and endemicity, and consequently highest priority of conservation, were the Lower Parana and Patagonia ecoregions. The Cuyan Desaguadero and Mar Chiquita Salinas Grandes ecoregions were the areas of second priority, and the Chaco and Lower Uruguay ecoregions were the areas with the third priority for conservation. Ten out of the 20 species analysed fall within the threat categories of the IUCN. Sixty per cent of the species of Aegla analysed have at least one population contained in protected areas.5. The results obtained may be used to design strategies for implementing conservation policies on freshwater species, generate biogeographical atlases and contribute to selecting Ramsar sites.