The material of Rotundomys (Rodentia, Cricetinae) from the Late Miocene fossiliferous complex of Cerro de los Batallones (Madrid, Spain) is described and compared with all species currently placed in the genera Rotundomys and Cricetulodon. Both the morphology and size variation encompassed in the collection of specimens from Batallones suggest they belong to a single taxon different from the other known species of these genera. A new species Rotundomys intimus sp. nov. is, therefore, named for it. A cladistic analysis, which is the first ever published concernig these taxa, has been conducted to clear up the phylogenetic position of the new species. Our results suggest that Rotundomys intimus sp. nov. inserts between R. mundi and R. sabatieri as a relatively primitive taxon inside the clade Rotundomys. The new taxon is more derived than R. mundi in having a transversal connection between the metalophulid and the anterolophulid on some m1 but more primitive than R. sabatieri and the most evolved species of Rotundomys (R. montisrotuni +R.bressanus) in its less developed lophodonty showing distinct cusps, shallower valleys, and the presence of a subdivided anteroloph on the M1. The species of Cricetulodon do not form a monophyletic group. As a member of Rotundomys, Rotundomys intimus sp. nov. is more derived than all of these taxa in its greater lophodonty and the complete loss of the anterior protolophule, mesolophs, and mesolophids.