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Large-bodied mole rats (Spalax) are a speciosus genus among obligate subterranean rodents, with seven currently recognized species, ranging from the Carpathians to the North Caucasus and further into the Caspian basin. Several conflicting hypotheses were proposed to explain the phylogenetic relationship among these taxa, mostly based on the subjective interpretation of the importance of certain morphologic characters in species delineation. We sequenced one mitochondrial (cytb) and one nuclear (IRBP) gene in six Spalax species, representing the most complete molecular dataset up to date. Both resulting phylogenies placed S. graecus, S. antiquus and S. giganteus at the base of the tree, while S. microphtalmus, S. zemni and S. arenarius appeared to have differentiated later in the evolutionary history of the genus. Cytb phylogeny supports monophyletic positions of all currently recognized species. According to the nuclear IRBP gene S. zemni and S. arenarius share similar haplotypes, which may represent either hybridization or recent separation from a common gene pool. The westernmost species S. antiquus and S. graecus represent the earliest split within the genus Spalax, indicating the possible origin of large-bodied blind mole rats from the South-West Europe. S. giganteus may represent the eastern relic of the ancient Spalax population. The central part of the genus distribution is inhabited by the most derived species: S. zemni + S. arenarius + S. microphthalmus. Large rivers of the Eastern Europe might have played a limited role in the distribution and speciation of mole rats and were crossed regularly by various genotypes. [ABSTRACT FROM AUTHOR]