The contemporary distribution of organisms cannot be understood without knowing how species have responded to the geologic and climatic history of their environments. Genetic studies related to the demographic history of wildlife species can help us to elucidate the role of climate changes and other environmental forces in shaping patterns of distribution and population structure of the species. In this work we investigated the phylogeographic pattern and historical demography of the subterranean rodent Ctenomys porteousi. We examined mitochondrial DNA control region sequences of 101 individuals collected from 7 localities that cover the complete distributional range of this species. Haplotype frequencies showed a significant population differentiation whereas the spatial distribution of haplotypes suggests moderate geographical structure. Genetic differentiation was not consistent with a simple model of isolation by distance and several independent estimates suggest that the observed phylogeographical pattern is the consequence of a complex demographic scenario. Our data suggest both reduction and population expansion events. Both kinds of demographic events were associated to major climatic changes that affected the study area during the Late Pleistocene and the Holocene. In particular, a relationship between historical changes in the degree of vegetation cover and population size for this rodent was inferred. We propose that the decrease in aridity of the Pampean region that started in the Pleistocene–Holocene boundary could have promoted a major decline in the effective population size of this species.