Mountain lakes, typical signs of an alpine landscape all around the world, were formed in the western part of the Carpathian Arch about 10,000-15,000 years ago, as remnants of the last continental glaciation. In the Tatra Mountains (Slovak-Polish border), more than 110 permanent lakes of glacial origin and many other small ponds exist. These (sub)alpine lakes, with their specific conditions, are very vulnerable and any change in their environment can largely impact their biodiversity, which is, despite long-term faunistic and ecological research, still not fully recognized. This shortcoming could be strongly improved by molecular approaches, which, even within population-genetic studies, often reveal unsuspected cryptic lineages or potential new species. Our long-term research is aimed at revealing the genetic diversity of aquatic macroinvertebrate species in the alpine environment of the Western Carpathians. One of the currently studied species is the glacial relict flatworm taxon Crenobia alpina (Dana, 1766) (Tricladida: Planariidae), representing an element of the permanent aquatic fauna. Totally, 88 COI haplotypes of C. alpina forming at least five well-separated genetic lineages were identified within 348 individuals collected from 45 lakes and ponds in theTatra Mts. Based on tests of selective neutrality and population stability, C. alpina populations in the Tatra lakes did not overcome recent population expansions or contractions. It seems that great genetic differences between localities and their population stability could be a consequence of the presence of natural topographic barriers (ridges, mountain peaks) dividing the mountains into small and relatively isolated valleys. Moreover, other important factors that could play a significant role are the limited dispersal ability of the species as well as its ability to reproduce asexually. Our findings were also compared with all publicly available sequences (Barcoding of Life Datasystems - BOLD and GenBank) in order to shift our data from a local to a holistic view on C. alpina. Our resultssupport the assumption of Brändle et al. 2017 that C. alpina represents a complex of cryptic lineages or species in Europe. As part of the AquaBOL.sk initiative, the data obtained contribute to the knowledge of genetic variability and barcoding of aquatic organisms in Slovakia.