The evolutionary history and systematics of blind mole rats (BMR), subfamily Spalacinae (Gray, 1821), are complicated by uneven geographic sampling and insufficient phylogenetic resolution provided by a few individual gene sequences. We combined genome-wide SNPs (ddRAD-seq) and mitochondrial cytochrome b (cytb) sequences with cytogenetic and biogeographic context to resolve the key phylogenetic relationships in this diverse group, using a large set of samples from different parts of the subfamily's entire geographic range. The previously resolved phylogeny within the Spalax (G & uuml;ndenstaedt, 1770) genus is confirmed and refined. In the genus Nannospalax (Palmer, 1903), all sampled populations and chromosomal forms were grouped into four major clades: three of them had originated and diversified in Anatolia and the Northern Levant, while the fourth colonized the European subcontinent. Molecular dating suggested that intensive divergence in all branches of the subfamily occurred within the past 1 Myr, but there was a pause in the speciation process after the Middle Pleistocene Transition, between approximately 0.6 and 0.4 Mya. Presently, multiple and highly divergent subclades are found in small and fragmented geographic ranges, but a few occupy large continuous territories and demonstrate comparatively low levels of genetic diversity.