The Myotis nattereri species complex has been the focus of several recent morphological and molecular surveys to assess the species status of various named forms, including three informally referred to as Myotis sp. A, M. sp. B and M. sp. C. The first two forms have now been formally described as distinct biological species, and named M. crypticus and M. zenatius, respectively, both distinct from the nominotypical M. nattereri s. str. and M. escalerai. The latter form, Myotis sp. C is known only from Corsica. Here we demonstrate that this form has not only unique mitochondrial haplotypes but also several nuclear alleles that are divergent and not found anywhere else, which emphasizes its long independent evolution. We therefore confirm its specific status and describe it as a new species. Its ecology and rupicolous roosting habits resemble those of the Iberian M. escalerai, but it is otherwise morphologically most similar to M. crypticus. This new species is endemic to Corsica and is apparently very rare and essentially localised to mountain forests. Owing to its restricted distribution, its small population size, and limited population connectivity, it seems highly vulnerable to climate change and thus should be classified as endangered.