After being presumed extinct, the blind mole rat was rediscovered in Vučedol, Croatia. Phylogenetic analyses using mitochondrial markers (cytochrome b and 16S rRNA) were conducted to classify the population. The results confirmed a distinct separation between the Lesser mole rats (Nannospalax leucodon clade) and Western mole rats (N. monticola clade). Within the N. monticola complex, six lineages were identified, which likely diverged during the Middle to Late Pleistocene. The Vučedol sample belongs to the montanosyrmiensis cytotype subclade, which was also found in Fruška Gora, Serbia. This subclade may represent a new species, showing K2P genetic distances of 4.3% to 5.7% from the "Pannonian Plain" subclade located on both banks of the Danube River. In two Pannonian localities, secondary contacts between populations of both subclades have been documented. One of them is the Kelebia –Subotička peščara population, where a unique subclade "Kelebia" was identified. Populations with montanoserbicus cytotype cluster within two distinct subclades, montanoserbicus A and montanoserbicus B, with K2P distances ranging from 4.6% to 5.3%, indicating potential species status for montanoserbicus A. In the most parsimonious network, montanoserbicus B exhibits a close relationship with the Pannonian Plain sublineage and a single sample from Bosnia and Herzegovina, showing K2P distances of 1.9% to 3.2%, suggesting that they may belong to the same species, N. monticola. Significant divergence between populations in Bosnia and Herzegovina highlights the need for further exploration of local variability and taxonomic status. Detailed analyses with additional markers from more localities are necessary before final species delimitation and taxonomic revision can occur. For now, Nannospalax monticola (Nehring, 1898) remains the sole valid name in the N. monticola complex.