We present the most comprehensive study to date of species groups in Ctenomys (tuco-tucos), a species-rich genus of Neotropical rodents. To explore phylogenetic relationships among 38 species and 12 undescribed forms we sequenced the complete mitochondrial cytochrome-b genes of 34 specimens and incorporated 50 previously published sequences. Parsimony, likelihood, and Bayesian phylogenetic analyses were performed using additional hystricognath rodents as outgroup taxa. The basal dichotomy of Ctenomys splits C. sociabilis from the remaining tuco-tucos, within which 8 main species groups were identified: boliviensis, frater, mendocinus, opimus, magellanicus, talarum, torquatus, and tucumanus. Whereas most of these groups refer to previous clades proposed on the basis of chromosomes or morphology, the torquatus and magellanicus species groups are novel taxonomic hypotheses. However, relationships among species groups are poorly resolved. Furthmore, the positions of C. leucodon, C. maulinus, and C. tuconax are conflicting or unresolved, and they might represent additional independent lineages. On the basis of molecular dating, we estimate that most species groups originated approximately 3 million years ago.