Taxonomic clarification of Tonnacypris stewarti comb. nov. (= Herpetocypris stewarti), a non-marine ostracod first described by Daday in 1908, was required due to the existence of various synonyms without detailed morphological descriptions. Our study examined specimens from Mang-tsa, Nam Co (Tibetan Plateau) and Lake Band-e Amir (Afghanistan). We identified seven definitive synonyms (Herpetocypris stewarti Daday 1908, Ilyodromus estonicus Järvekülg 1960, Eucypris afghanistanensis Hartmann 1964, E. gyirongensis Yang 1982, E. rischtanica Schneider 1963 in Mandelstam & Schneider 1963, Tonnacypris estonica (Järvekülg 1960), and T. gyirongensis (Guo et al. 2016). After a detailed study of the morphology of valves and soft parts supplemented by a literature review, we propose combining the genus Tonnacypris with the specific epithet stewarti, resulting in the new name Tonnacypris stewarti. We documented the ontogenetic series of T. stewarti in surface sediment samples from Nam Co. Only female specimens were found, consistent with observations in Mongolia, where they were considered asexual populations. Sexual populations were reported from Afghanistan and the southern Tibetan Plateau, suggesting geographic parthenogenesis in the Palearctic region. Because of widely missing males, we explored the use of female genital lobes as a distinguishing feature for taxonomy. Considering current ecological knowledge, T. stewarti could serve as a (paleo)—bioindicator of cold, oligotrophic, and fresh to slightly brackish habitats, including rivers, lagoons, and lakes. This study emphasizes the importance of resolving taxonomic issues for future paleolimnological research. Moreover, our investigation highlights the potential use of sclerotized internal female genital lobes as distinctive characteristics for species differentiation, especially in asexual populations.