Various bat species often occupy the same habitats. Cohabitation should induce different preferences in spatial or trophic components of the bat ecological niche to reduce their competition. This determines the differences in the trematode fauna of Myotis spp. The purpose of our research was to study the biodiversity of trematodes in syntopic populations of five Myotis species in the Samarskaya Luka National Park. In the 2005–2007 period, we studied 867 bat specimens via the methods of complete helminthological dissection. In total, 11 trematode species from the families Plagiorchiidae (Plagiorchis koreanus, P. mordovii, P. muelleri, and P. vespertilionis), Pleurogenidae (Parabascus duboisi), and Lecithodendriidae (Prosthodendrium ascidia, Pr. chilostomum, Pr. cryptolecithum, Pr. hurkovaae, Pr. longiforme, and Lecithodendrium linstowi) were found in five Myotis species. Only three trematode species, P. koreanus, Pr. chilostomum, and P. duboisi, are common to all studied Myotis spp. Prosthodendrium cryptolecithum was recorded for the first time in Russia. Trematode species diversity is higher in Myotis daubentonii and M. dasycneme. The trematode fauna of M. brandtii, M. nattereri, and M. mystacinus is less diverse. The determining factor in the infection of bats with trematodes is feeding on semi-aquatic insects, possible second intermediate hosts of the parasites. The infection of bats with flukes occurs at different levels of host (Myotis spp.) abundance as a result of the realization of the main bat trophic relationships. Our results confirm the data that the ecological niches of the five Myotis species partially overlap. Analysis of the trematode fauna in Myotis spp. showed that, in the Samarskaya Luka, there may be weak competition for food items among bats.