The red viscacha rat, Tympanoctomys barrerae, is an octodontid rodent endemic to the arid west-central and southern regions of Argentina. It is solitary, lives in complex burrows built in soft soil, and occurs at low population densities in patches associated with salt basins and sand dunes in lowland habitats of the Monte and Patagonia deserts. The purpose of this study was to investigate the genetic structure and biogeography of this desert specialist. To assess genetic variation an 800-base pair fragment of the mitochondrial control region was sequenced for 60 individuals from 8 localities across the species' range. Relationships among haplotypes were inferred from phylogenetic analyses (maximum parsimony, Bayesian, and networks). Genetic structure and demographic history were analyzed with descriptive statistics, mismatch distributions, neutrality tests (Tajima's and Fu's), and analyses of molecular variance (AMOVAs). In total, 26 haplotypes were found, most restricted to single populations. The presence of unshared haplotypes was consistent with low migration rates. Within the distribution (between 29°S and 39°S) southern and northern populations showed higher genetic diversity values than central populations. Populations of T. barrerae showed moderate to high genetic differentiation on the basis of haplotypes of central populations. AMOVA analyses indicated a moderate level of geographic structure for all populations. Low haplotype and nucleotide diversities in central populations suggest a possible bottleneck associated with Pleistocene glaciations or volcanic activity in this part of the range of the viscacha rat. Phylogeographic structure was moderate, and the analyses recovered 2 principal clades: A (with central and a part of the southern distribution) and B (with northern and another part of the southern distribution). Most populations were polyphyletic, indicating that they have not been isolated long enough to reach reciprocal monophyly. Demographic analyses conducted for clades A and B suggest a recent history of population expansion.