A new population of blind mole rat (genus Nannospalax) was discovered near the town of Albertirsa in north-central Hungary. We used newly designed primers to specifically amplify the whole mitochondrial cytochrome-b region and two nuclear DNA regions. Based on the most comprehensive taxonomic sampling to date, we compared this population with several other European blind mole-rat taxa. The results from both mitochondrial and nuclear regions have unequivocally placed the Albertirsa population into the monophyletic group of the Vojvodina blind mole rat (N. (leucodon) montanosyrmiensis), which turned out to be a sister clade to all other molecularly studied European Nannospalax. This study not only identified the fourth known population of an extremely rare rodent taxon but also calls for a taxonomic revision of European lesser blind mole rats (N. leucodon superspecies) to systematically evaluate the genetic structure of their populations and to understand the complex evolutionary history of these European rodents. The occurrence of the Vojvodina blind mole rat at this northern location helps to clarify the distribution area of this heavily data-deficient taxon. As currently understood, this lineage predominantly occurs in sandy grasslands of the Danube–Tisza Interfluve in Hungary and Serbia. Its distribution range and phylogenetic structure might reflect the importance of potential biogeographical barriers (e.g. large rivers) that shaped the blind mole rats' allopatric or peripatric speciation.