Cryptogenic species are those whose native and introduced ranges are unknown. The extent and long history of human migration rendered numerous species cryptogenic. Incomplete knowledge regarding the origin and native habitat of a species poses problems for conservation management and may confound ecological and evolutionary studies. The Lesser Antilles pose a particular challenge with regard to cryptogenic species because these islands have been anthropogenically connected since before recorded history. Here, we use population genetic and phylogeographic tools in an attempt to determine the origin of Eleutherodactylus johnstonei, a frog species with a potentially widespread introduced range and whose native range within the Lesser Antilles is unknown. Based on elevated estimates of genetic diversity and within-island geographic structure not present elsewhere in the range, we identify Montserrat as the native island of E. johnstonei. We also document two major clades within E. johnstonei, only one of which is the primary source of introduced populations throughout the Americas. Our results demonstrate the utility of genetic tools for resolving cryptogenic species problems and highlight E. johnstonei as a potential system for understanding differences in invasive potential among sister lineages.