Ecological speciation is an evolutionary process driven by divergent natural selection in heterogeneous environments characterised by diverse resources and habitats. Increasing evidence supports the occurrence of this phenomenon in nature. One frequently cited example among mammals is the Upper Galilee Mountains blind mole rat, Nannospalax galili. Over a decade ago, it was proposed that this species is undergoing incipient ecological speciation due to the sharply contrasting ecological conditions resulting from the presence of pale rendzina and dark basaltic soils. In this study, we examined the population genetic structure and gene flow between mole rats inhabiting these two distinct soil types at two localities in Northern Israel, Rihaniya and Gush Halav, each containing sites on both rendzina and basaltic soil types. We used eight microsatellite markers to assess genetic differentiation. The results indicate that in Rihaniya, where blind mole rats from both soils were sampled in close proximity, the genetic divergence between animals from the different soil types was the lowest. In Gush Halav, the genetic differentiation increased with geographic distance between sampled sites, indicating an isolation-by-distance effect. The presence of migrants and first-generation hybrids in both soils at both localities suggests that blind mole rats migrate and mate relatively frequently between the two soil types. These findings imply that ecological speciation in N. galili may be in its very early stages, with no clear evidence of assortative mating yet. Further research is needed to understand this phenomenon in this study system.