In this study, parasite species from different bat species were investigated. A comparison of the communities of trematodes occurring across Swiss bat species was carried out. An updated checklist compiling the parasitic helminths that occurs in bats across Europe was established, with 122 different parasite species recorded from previous studies, whilst the total putative parasite richness across European bat species is of 197 species, suggesting a significant number of species yet to be uncovered. A total of 75 bats belonging to 16 different species were examined for metazoan parasites, for a total of 4890 specimens recovered from those samples. Among 176 examined samples, nine different trematode species were confirmed through molecular analyses. Among those species, both Lecithodendrium linstowi, Plagiorchis koreanus and P. vespertilionis were confirmed by morphological identification. These trematodes were recovered from various bat species, which indicates a rather low host specificity for these helminths, and therefore demonstrates the characteristic of generalist species. The initial hypothesis that there is a limited number of generalist parasite species and that more cryptic species were yet to be discovered was rejected. A structure of populations within the parasite species could not be observed using intraspecies molecular markers (ITS and COI). The number of lineages correspond to the number of uncovered species.