Both the Cytb gene of mtDNA and Y chromosome markers were studied in a relatively large sample of brown hares (L. europaeus) from Europe and Anatolia (Turkey and Israel), together with other seven Lepus species, in order to enable comparative analysis of possible sex-specific gene flow. Furthermore, Y chromosome markers were compared with data from biparentally inherited markers in an attempt to understand whether or not their pattern of distribution was congruent with that of allozymes or whether they rather matched mtDNA phylogenies, with which they share uniparental inheritance. Consistent with the general observation, levels of interspecific genetic variability were very low for the Y chromosome markers compared with mtDNA. Moreover, lack of interspecific variation for the Y-DNA studied within Lepus genus rendered these markers improper for any further phylogenetic analysis. With the highest nucleotide diversity in Anatolia compared with Europe, both marker systems confirmed an unbroken species history in Anatolia, corroborated the hypothesis of continuous gene flow from Anatolia's neighbouring regions, and supported the idea of a quick postglacial colonization followed by expansion of the species in large parts of Europe. Phylogenetic analysis under mtDNA revealed the existence of four different haplogroups with a well defined distribution across Europe and Anatolia. Both genetic systems supported the deep separation of Anatolian and European lineages of L. europaeus. Nevertheless, Anatolian Y-DNA lineages extended across a longer geographic distance in south-eastern Europe than Anatolian mtDNA haplotypes, probably as a result of higher female philopatry that makes mtDNA introgression more difficult in brown hares. (C) 2009 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.