The contemporary geographical distribution and genetic structure of temperate species have been strongly influenced by the climatic oscillations during the Late Quaternary. As spatial genetic reconstructions are often markedly affected by geographically meaningful sample distributions, we focused in our study on the analyses of mtDNA control region sequences of brown hares from different regions in northern, central and south-central Balkans that have so far not been covered, with the aim to delineate the most likely glacial refugia wherefrom the postglacial northward expansion into central Europe has originated. Three major haplogroups (“Anatolia/Middle East”, "the Balkans", and “central Europe”) were revealed with apparent south-north gradual decrease in molecular diversity indices. Moreover, phylogenetic and demographic history analyses identified the southeastern central Balkans as the putative origin for most populations from the southern and northern Balkans, while populations from central and northwestern Europe have originated from the northern Balkans.