Abstract. The freshwater flatworm Crenobia alpina (Platyhelminthes, Tricladida, Planariidae) lives almost exclusively in cold springs and crenal streams and possesses only limited dispersal ability. In this study fragments of the COI and 18S rRNA genes were used to estimate genetic divergences among 37 C. alpina populations from the European Alps. Phylogenetic analyses revealed five geographically and genetically distinct groups and at least 10 distinct lineages of C. alpina across the European Alps. Our study suggests that C. alpina represents a complex of numerous cryptic species. Speciation (allopatric and/or sympatric) may have been facilitated by the orogenetic activity of the Alps and the high habitat specificity.