<p>In mammals, subterranean lifestyle is thought to be associated with limited dispersal ability and low effective population size. These characteristics are expected to increase both inter- and intrapopulation differentiation while reducing intra-population genetic diversity. However, the available empirical data indicate this pattern is not universally applicable. Expanding the range of studied taxa and comparing between populations of the same species can contribute to our understanding of the factors responsible for the genetic dynamics. Previously unexamined in this context, the northern mole vole (<i>Ellobius talpinus</i>) shows promise as a model species for population genetics due to its broad geographic range and habitat plasticity, and variation in breeding system. Here, we present the first assessment of the genetic patterns in <i>E. talpinus</i> and compare the levels of genetic diversity of two distant populations. As expected, the highly fragmented Novosibirsk population from the extreme northeast of the species’ range showed low microsatellite diversity (observed heterozygosity, <i>Ho</i> = 0.34 and unbiased expected heterozygosity, <i>uHe</i> = 0.55). The mitochondrial D-loop was nearly monomorphic with a haplotype diversity (<i>Hd</i>) of 0.14. In contrast, the subperipheric Saratov population displayed moderate nuclear (<i>Ho</i> = 0.64; <i>uHe</i> = 0.76) and high mitochondrial variation (<i>Hd</i> = 0.83), compared to the surface-dwelling voles. In a heterogeneous landscape, significant genetic differentiation was revealed at both intermediate (dozens of kilometers) and small (several kilometers) scales. However, within continuous suitable habitat, no fine-scale (within 1000&#xa0;m) spatial structure was detected, except for that resulting from kin clustering.</p>