The genus Bythinella comprises many species throughout Europe, but species delimitation, traditionally based on shell morphology and genital anatomy, is often a matter of debate. Out of an ongoing large-scale project on the phylogeny of the genus, we analyzed the relationships of species occurring in the south Austrian province Carinthia and in neighboring Slovenia as a model for similar cases of systematic and taxonomic ambiguity. Our analyses based on sequence data of a fragment of COI comprising 638 bp, morphological and anatomical investigations confirmed the presence of three species, B. opaca (Gallenstein, 1848), B. robiciana (Clessin, 1890) and B. angelitae nom. nov. for B. opaca (Frauenfeld, 1857). The latter, while genetically distinct, is morphologically and anatomically cryptic in that it can only be distinguished from B. opaca by the denticulation of the radular marginal teeth. B. robiciana, on the other hand, is morphologically well defined, but genetically not separable from B. opaca, its stem species. Thus, taxonomy in Bythinella has to be based on the integration of morphology, anatomy and genetics. Our phylogenetic analyses suggest that B. opaca has colonized Carinthia, which has largely been covered by glaciers during the last ice age, along two routes, one from the south and a second one from the southeast.