The temperate rain forest of Chiloé Island, Chile, is inhabited by an endemic fox (Dusicyon fulvipes) first described by Charles Darwin and now designated Darwin’s fox. Despite morphological differences, Darwin’s fox has been considered only an insular subspecies of the mainland chilla fox (D. griseus). This follows the assumption that the island population, with an estimated population of less than 500, has been separated from the mainland chilla fox for only about 15,000 years and may have received occasional immigrants from the mainland. Consequently, this island population has not been protected as endangered or bred in captivity. Recently, a population of Darwin’s fox was discovered on the Chilean mainland 600 km north of Chiloé Island. This population exists in sympatry with chilla and possibly culpeo (D. culpaeus) foxes, which suggests that Darwin’s fox may be reproductively isolated. To clarify the phylogenetic position of Darwin’s fox, we analyzed 344 bp of mitochondrial DNA control‐region sequence of the three species of Chilean foxes. Darwin’s foxes from the island and mainland populations compose a monophyletic group distinct from the two other Chilean fox species. This indicates that Darwin’s fox was probably an early inhabitant of central Chile, and that its present distribution on the mainland may be a relict of a once much wider distribution. Our results highlight the ability of molecular genetic techniques to uncover historical relationships masked by recent events, such as local extinctions. The “rediscovery” of Darwin’s fox as a distinct species implies that greater significance should be given to the protection of this species and its unique habitat and to documenting the extent of its mainland distribution.