The South American Ctenomys is the most speciose genus among both hystricomorphs and subterranean rodents of the world. Here, we present the most exhaustive phylogenies and timetree of living and extinct Ctenomys attempted thus far. We describe Ctenomys rusconii sp. nov., a small-sized species from the upper Early Pleistocene of central Argentina. We analyse its cranial and mandibular shape as well as its phylogenetic position in the context of other extinct Ctenomys and a wide sample of living species. A parsimony analysis shows that Ctenomys rusconii sp. nov. integrates the stem group of Ctenomys together with late Pliocene to Middle Pleistocene species, while the crown group comprises only Middle Pleistocene to recent representatives. Within the crown Ctenomys, nine well-supported major clades were recovered, eight of which are consistent with previously recognized extant species groups. A Bayesian tip-dating analysis provided divergence age estimates of 3.8 Ma and 1.3 Ma for the origin of the genus and the crown clade, respectively. Remarkably, the extinct species recovered as members of the crown clade, i.e. C. dasseni, C. kraglievichi, C. subassentiens and C. viarapaensis, were clustered into the earliest diverging clade corresponding to the frater species group. Age estimates for the divergence of the crown and its major clades are markedly younger than what has been generally considered so far, which implies a new view on the timing of taxonomic, ecological and geographical diversification of the genus. Even considering that this interpretation is affected by biases inherent to the fossil record, the phylogenetic delimitation of the crown clade as restricted to species recorded since the Middle Pleistocene seems to configure a pattern underlain by a fast and late cladogenesis. http://zoobank.org/urn:lsid:zoobank.org:pub:14D8C3B2-CD37-4F30-84A2-14FDC20F1193