Spalacopus cyanus is a subterranean rodent inhabiting coastal and mountain habitats. Individuals from mountain populations are larger than individuals from the coast, and mountain populations have a more limited geographic range. To investigate the genetic structure and biogeography of this species, we analyzed mitochondrial DNA control region sequences. We found low levels of nucleotide diversity in comparison with other subterranean rodents. Coastal populations had higher nucleotide diversity and effective population size than mountain populations. Phylogenetic analysis using maximum parsimony and a haplotype network generated using statistical parsimony recognized 3 groups of haplotypes: northern coastal and mountain populations, central coastal populations, and southern coastal population. Consistent with the presence of unshared haplotypes, migration rates were practically 0, except from Valparaíso to Ventanas and from La Parva to Huentelauquén. We observed asymmetric migration rates from mountain to coastal populations, suggesting that this species originated in the Andean mountains. A likelihood ratio test could not reject the null hypothesis of a stable population when all sequences were grouped into a single population and when coastal populations were analyzed separately. However, a negative exponential growth parameter was estimated for mountain populations, suggesting that these populations have undergone recent demographic changes.