Lowland Leopard Frogs (Rana yavapaiensis) have experienced extensive population declines over the last century. In California, this species was historically known to occur in scattered localities in the extreme southeastern portion of the state, but it has not been positively documented since 1965. Subsequent to this decline in California, nonnative Rio Grande Leopard Frogs (R. berlandieri) have expanded into localities previously occupied by R. yavapaiensis. The lack of extensive formal surveys and the difficulty distinguishing between these species using morphological characters have caused uncertainty about whether Lowland Leopard Frogs persist within their historical range in California. Recently, leopard frogs that could not be confidently identified to species have been observed at historical localities of R. yavapaiensis. Thus, we undertook a formal study of these populations to characterize their morphological and genetic variation, and conclusively determine to which species they belong. Our genetic analyses demonstrate that these frogs are R. berlandieri, but the morphological characters typically used to diagnose these species are largely overlapping. Further complicating field identifications, for some morphological characters, the California R. berlandieri are more similar to R. yavapaiensis than to native-range R. berlandieri. Additionally, invasive R. berlandieri show greater variation in a key character—the condition of the inset dorsolateral folds—than that found across much of the species' native range. These results demonstrate the potential for morphological change during rapid population expansions to confound species identifications. Our findings have implications for future efforts to resolve the status of R. yavapaiensis in California and to identify other native leopard frogs found within the expanding range of R. berlandieri. Our results also highlight the utility of genetic approaches for reliably identifying morphologically similar leopard frogs.