Many trematode groups have a long history of systematic revision, which can make parasite identification a difficult task. The trematode parasites of muskrats are no exception. Here, we highlight the systematic issues associated with trematodes of muskrats (Ondatra zibethicus). Then, we demonstrate the utility of using both morphological and molecular tools to identify these parasites. Morphological examinations of specimens from muskrats (n = 63) first suggested that at least 4 genera were present including Echinostoma, Wardius, Quinqueserialis, and Notocotylus. For the latter 3 groups, the 28S region verified this assessment. For echinostomes, ND1 sequences revealed at least 5 genetic lineages. A particular lineage, Echinostoma trivolvis lineage b, predominated in both prevalence and intensity of infection. Molecular sequences provided a more accurate estimate of echinostome diversity in the muskrats and further support the idea that E. trivolvis is a species complex. Future studies will focus on whether there are differences in host specificity among the E. trivolvis lineages. In addition, this study has provided initial sequences that will help verify the life cycles of Wardius, Quinqueserialis, and especially, Notocotylus. By linking molecular, morphological, and life history information, we can better understand parasite diversity.