In Europe, distribution of many animal species has been severely restricted to small refugia during the last glacial period. The Balkan Peninsula including Bulgaria has been identified as one of the three main glacial refugia (Randi 2007). To know biogeographical history in Europe, molecualr phylogeographical studies about various European mammal species have been performed: for example, the least weasel Mustela nivalis by the mitochondrial DNA (mtDNA) control region and cytochrome b (Lebarbenchon et al. 2010), the ground squirrel Spermophilus citellus by cytochrome b (Krystufek et al. 2009), the yellow-necked fieldmouse Apodemus flavicollis and the woodmouse A. sylvaticus by cytochrome b (Michaux et al. 2005), the brown bear Ursus arctos by mtDNA control region (Taberlet and Bouvet 1994; Taberlet et al. 1998) and the hedgehogs Erinaceus europaeus and E. concolor by cytochorome b (Santucci et al. 1998). These studies commonly show that distribution of European species was influenced by climate changes in the Quaternary glaciations, and they survived in different ways (Michaux et al. 2005). Studies on the genetic diversity of mammals in Bulgaria as part of the Balkan Peninsula provides further insights to understanding of biogeographical history from the last glacial maximum (LGM) to present in south Europe. The stone marten Martes foina is a medium-sized carnivore of the family Mustelidae, and is distributed from Spain and Portugal in the west, through central and southern Europe, the Middle East, and central Asia, extending as far east as the Altai and Tien Shan Mountains and northwest China (Abramov et al. 2006). This species prefers more open areas than other martens (Sacchi and Meriggi 1995). Its habitat preferences vary in different parts of its range. Martes foina is typically found in deciduous forests, forest edges and open rocky hillsides. In some areas, however, M. foina also inhabits suburban and urban areas, with rare woods (Tikhonov et al. 2008). Because the Balkan Peninsula is one of the southern limit of distribution of M. foina, the analysis of its Balkan population would contribute to further understanding of refugia and phylogeography in Europe. Whereas there have been some phylogenetic studies about the family Mustelidae including M. foina (Marmi et al. 2003; Li et al. 2011) and a microsatellite variation study of M. foina in southern Portugal (Basto et al. 2010), no population genetic studies about this species in Bulgaria have been reported. In the present study, to know the population structure and phylogeography of the Bulgarian population of M. foina, we studied its microsatellite polymorphisms and mtDNA control region variation, and then discuss the genetic diversity in the population.