Martes foina is a member of the family Mustelidae, found throughout Europe and central Asia. Attempts to study the genetic structure and the phylogeography of European M. foina populations have been recent, none of which took place in Greece. The present work aims to 1 ) study the genetic diversity of Greek Martes foina populations, 2) analyze the geographical distribution of the resulting lineages and 3) examine the existence of genetic support behind the presently accepted M. foina subspecies. Analyses carried out on 54 mitochondrial DNA sequences (1468 bp) consisting of almost the entire cytochrome b gene (928 bp) and part of the mitochondrial control region (540 bp) indicate towards a demographic expansion of the species, which could be attributed to the existence of an ice age refugium in Greece during the Last Glacial Maximum. The haplotype and nucleotide diversity was found greater than in other studies on M. foina reinforcing the scenario of Greece being a biodiversity hotspot. The 18 different haplotypes that were found clustered in two clades, hinting towards the presence of more than one separate subrefugia within the Balkans. With respect to the genetic support for subspecies, the genetic distances calculated among all subspecies were not capable to support their existence. In the case of the Rhodes population, which has been designated as a distinct subspecies (M. foina milleri), only the clustering of haplotypes allows us to differentiate that island population from the rest.