Water frogs inhabiting Cyprus represent a distinct evolutionary species of Messinian origin that is formally described in this paper. The systematic status of Cypriot frogs is evidenced by specific characters in their mitochondrial (mt) and nuclear (nu) DNA sequences, and the fact that they form a well supported monophyletic clade in both mtDNA and nuDNA phylogenies. While genetic data revealed clear and reproducible differences between this new taxon and all other western Palearctic water frog species including Pelophylax bedriagae in the Levant and two Anatolian water frogs lineages (P. cf. bedriagae -1 and P. cf. bedriagae -2), there is no diagnostic morphological or morphometric character that allows a clear discrimination between Cyprus frogs and frogs from the adjacent mainland. If several morphometric indices are combined as predictor variables in a discriminant analysis, however, both females and males of Cypriot water frogs are correctly distinguished from the other eastern Mediterranean lineages. While phylogenies based on concatenated sequences of two mitochondrial genes (ND2 + ND3) suggest a sister group relationship of Cypriot and Anatolian water frog lineages, our nuclear data hypothesize a sister group relationship between Cypriot frogs (sp. n.) and Crete frogs (P. cretensis), thus speaking for the same isolation time of both island populations