Freshwater snails are important intermediate hosts for several parasitic diseases, including fascioliosis and schistosomiosis, with significant impacts on human and animal health. In Bangladesh, vector snails have been identified only by morphology. Here, we validate the species of freshwater snails acting as intermediate hosts for Fasciola and Schistosoma spp. using molecular and bioinformatics tools. Following morphology and morphometrics, we identified 9 species of snails: Lymnaea auricularia, Lymnaea luteola, Indoplanorbis exustus, Physa acuta, Viviparus bengalensis, Brotia spp., Thiara spp. and Pila globosa. Cercarial shedding tests revealed that L. auricularia (0.72%, 7 out of 977) and L. luteola (0.36%, 8 out of 2240) shed fasciolid cercariae, which polymerase chain reaction (PCR) confirmed. But I. exustus (5.43% 19 out of 350), L. auricularia (9.42%, 92 out of 977), L. luteola 10.09% (226 out of 2240), P. acuta (2.4%, 11 out of 450) and V. bengalensis (0.14%, 7 out of 500) shed schistosomatid cercariae. The same snail did not shed both fasciolid and schistosomatid cercariae simultaneously. PCR and sequencing of the Cox1 gene confirmed the species of the intermediate hosts. The sequences of L. auricularia, L. luteola, I. exustus, P. acuta and V. bengalensis were identical (99−99.7%) to reported sequences of these species. Phylogenetic analysis revealed that sequences of the present study for each species formed well-separated clusters with the corresponding reference sequences. Taken together, the results of this study highlight the importance of molecular tools for confirming snail species and will help target specific vector snails in the particular habitat when designing snail-borne trematode control programs.