Morphological patterns among species of the genus Rutilus from the southern Balkan Peninsula were analysed to identify morphological differentiation and its palaeogeographic history. Seven meristic and 65 morphometric characters, based on 20 landmarks, were studied on 711 specimens from 15 Greek lakes. Multivariate analyses demonstrated a well-supported differentiation of the western and northern from the eastern Rutilus species' populations, separated by the Pindos Mountains. In North-western Greece, there are three isolated endemic species, in different biogeographical areas (R. prespensis in the Southern Adriatic, R. panosi in the Ionian and R. ylikiensis in the Attico-Boeotia), while in the Northern Aegean, multiple non-homogeneous populations of the cosmopolitan R. rutilus can be found. This distribution is clearly in accordance with the biogeographical scenario for the distribution of freshwater fauna of the Balkan Peninsula. This study confirms differentiation of the populations of Lakes Kastoria, Volvi, Vegoritida and Doirani, and emphasizes the likely existence of cryptic species within R. rutilus populations.