Host specificity is essential to understanding the ecology and evolution of parasites, and it is often complicated to estimate because of the presence of morphologically similar but genetically distinct species. Morphological identification of larval trematodes is often challenging because of the lack of diagnostic characteristics that only appear in the sexually mature adult stage. The difficulty in accurate species identification may obscure their compatibility with the host species. We investigate the parasites infecting 2 Asian mud snail species, Batillaria multiformis and Batillaria attramentaria, at 1 site where the 2 host snails co-occur to identify the level of their host specificity. We found that the morphospecies Cercaria batillariae was the most common trematode species in B. attramentaria and B. multiformis. We conducted polymerase chain reaction (PCR) –based restriction fragment-length polymorphism (RFLP) analyses of 77 C. batillariae infections in B. attramentaria and 150 in B. multiformis. We further sequenced the representative RFLP patterns to evaluate their phylogenetic relationship. We observed 6 genetically distinct species infecting 2 host species. Of those, 2 parasite species exclusively infected B. attramentaria, and 1 was found only in B. multiformis. Although 3 parasite species infected both hosts, 2 of them showed highly biased infections to either host species. Our study suggests that trematodes in the Batillaria snails can be host specific and highlighted the usefulness of molecular genetics for assessing host specificity.