The rock partridge (Alectoris graeca) is distributed in the Alps, Apennines and Balkans, in mountainous areas that were heavily affected by cyclic climate and landscape changes during the last Pleistocene glaciations. Some partridge populations have colonized and expanded their present ranges only after deglaciation and recent deforestation by humans. Other populations have been segregated in land-bridge islands isolated after the rise in level of the Mediterranean Sea. Consequently, partridges from different areas could be genetically differentiated. This study has analysed 436 nucleotides of the domain I of the mitochondrial DNA control-region in 70 rock partridges collected from 14 populations throughout their distribution. Phylogenetic analysis and analysis of molecular variance showed that the Sicilian population is very divergent from the continental populations. The Albanian and central Apennine samples are slightly divergent from the Alpine rock partridges, which cluster in two groups according to their east-west distributions. The mitochondrial DNA sequences suggest the existence of a phylogeographical structuring among rock partridge populations, resulting from genetic divergence in southern refugia and subsequent postglacial colonization of northern mountain areas. Sicilian partridges could have been isolated for ≈500 000 years, whereas the Albanian-Apennine populations could have been in contact since the last glacial maximum (21 000 yr BP) through the north Adriatic land-bridge. The Alps could have been colonized in two different periods or by two different source populations. The mitochondrial DNA phylogeographical structuring is not completely concordant with the subspecies distribution. These findings suggest that rock partridges should be managed based on the identification of phylogeographical units.