The house mouse (Mus musculus domesticus) and the short-tailed mouse of the eastern Mediterranean area (M. macedonicus) were thought to live sympatrically on Cyprus Island. Recently, a phylogenetic survey has shown that the non-commensal mouse of Cyprus was an unknown sister species of European wild mice. Here, we describe this new species of the genus Mus (Rodentia, Mammalia), namely Mus cypriacus sp. n., based on 19 specimens trapped in the southern part of Cyprus. These animals were first compared to Eurasian species of mice using both molecular genetics (complete D-loop sequences and nuclear gene intron) and cytogenetics to state on its systematic status. Then classical and geometric morphometric analyses on both cranial and dental characters have been performed to compare Mus cypriacus with circum-Mediterranean species and provide diagnositic morphological characters. Genetic data strongly support a sister species relationship of the new species to M. macedonicus, the closest mainland taxon. Morphometric analyses provide satisfying criteria for diagnosis of this species relative to other Mediterranean species. The most obvious phenotypic characteristics are its long tail and the allometric gigantism and shape robustness of its cranial and dental characters compared to other Mediterranean mice. The molecular clock and the history of the murine settlement on Cyprus are congruent and suggest that the common ancestor of M. cypriacus and M. macedonicus arrived on Cyprus during the Middle Pleistocene by a founder event on natural raft. The remoteness of Cyprus through time has prevented introgression from the mainland gene pool, and favoured phenotypic adaptation to competition release, leading to the allopatric speciation of M. cypriacus.