The taxonomic history of the species of Plagiorchis Lühe, 1899 occurring in European bats has been very confused because of high morphological similarity between different forms/species and the inadequate initial description of P. vespertilionis(Müller, 1780). As morphological data alone have not provided enough convincing arguments to solve the problem, the sequences from the nuclear rDNA ITS region (ITS1, 5.8S and ITS2) of three species of the P. vespertilionis group (P. vespertilionis, P. muelleri Tkach & Sharpilo, 1990 and P. koreanus Ogata, 1938) occurring in European bats were used to test the validity of these species and evaluate some of the morphological characters used for the species differentiation within this group. P. elegans from birds was used as the outgroup in the analysis. All three ingroup species were clearly distinguishable using ITS sequences. Among them, P. koreanus occupied a basal position, while P. vespertilionis and P. muelleri appeared as a cluster of two closely related, derived species. ITS sequences of the specimens obtained from different hosts and/or geographical areas did not exhibit any intraspecific variability. Morphological study of the material in collections revealed characters which enable the species of Plagiorchis from bats in Europe to be distinguished. Taking into account that the type-material of P. vespertilionis, described during the 18th Century, has been lost, for nomenclatural stability, a neotype is established and described. An amended description of the type-material of P. muelleri and keys for the determination of Plagiorchis spp. from European bats are presented.