We found metacercariae of a microphallid trematode Atriophallophorus minutus in freshwater snails Bithynia tentaculata. In this study, we provide a morphological description of whole-mount specimens and semi-thin sections of experimentally grown adults of this species. Our morphological examination supports the idea that the adults of Atriophallophorus spp. have a ventral sucker with a sinistral interruption of the outer edge. In the 28S rDNA gene-based phylogenetic analyses, our specimens of A. minutus were grouped into Atriophallophorus spp. clade, as a sister taxon to Atriophallophorus winterbourne + Atriophallophorus sp. Analysis of the pairwise genetic distances between coI mtDNA gene sequences revealed a low divergence between the two specimens of A. minutus (1.1%) and a greater divergence (up to 16.6%) between them and A. winterbourni. Since other Atriophallophorus spp. are known to have a strict specificity to the polyvalent intermediate host, we suggest that A. minutus reported from different snail species may represent a complex of cryptic species.