Two species of ostracods new to Patagonia, Argentina, are described. One of them, Riocypris whatleyi sp. nov., is described for the first time, and the second, Riocypris sarsi (Daday, 1902) comb. nov., is reallocated from genus Eucypris to genus Riocypris. Inter- and intra-specific variations in shape, size, and sexual dimorphism were evaluated based on geometric morphometric analysis. Moreover, morphological and morphometric comparative analyses were applied to re-examine living and quaternary specimens recovered from previous studies. Based on these results, a generic reassignment for the Patagonian Eucypris fontana (Jurine, 1820) into the genus Riocypris is proposed. Contributing to the knowledge on the systematic and autecology of this enigmatic species, widely distributed in Patagonia and frequently used in paleolimnological reconstructions, generates science-based evidence for their use as indicator species. Additionally, our results emphasize the usefulness of studying the living representatives (i.e., with valves and appendages) for elucidating the taxonomic status of the individual specimens, especially those present in paleontological records and used as bioproxies in paleolimnological studies.