The phylogenetic relationships within the passerine family of Buntings (Emberizidae) are relatively well investigated, but below the species level there are some gaps especially in taxa of the eastern Palearctic. In case of the Black-faced Bunting Emberiza spodocephala, three subspecies have been described. Two of them ? E. s. spodocephala and E. s. personata - are morphologically distinct taxa and are sometimes listed as separate species. In this study we investigate the taxonomic relationships and phylogeographic history of this subspecies complex by combining morphometric and molecular genetic data. 138 individuals of E. spodocephala were captured in Far Eastern Russia. All birds were measured (wing, p8, bill, tarsus) and a DNA-sample (feather) was taken. Additionally, 317 museum specimens were measured and 20 DNA samples were obtained at the Bird Collection NHM London. Differences in DNA were examined by sequencing the mitochondrial CO I gene and the nuclear sex-linked CHD1Z gene. Tarsus and bill length were the most differentiated morphometric measurements with significant differences between all examined subspecies. Due to the great extent of overlapping however the biological relevance and benefit for field identification is under question. Investigation of mitochondrial DNA showed a deep divergence between E. s. spodocephala and E. s. personata indicating a population split around 1.5 million years ago. In one case, the assignment to one subspecies through mtDNA did not match the identification by plumage traits. This individual, who resembled a male of E. s. spodocephala in breeding plumage without any sign of intermediacy, could be a sign for introgressive hybridization. Investigation of nuclear DNA yielded significant population differentiation between the two subspecies. We conclude that the two subspecies follow a general phylogeographic pattern in the Eastern Palearctic, in showing deep divergence between the island and mainland form.