We present new remains of Pachyrukhinae (Hegetotheriidae) from the Huayquerías del Este (Mendoza, Argentina). We identify Tremacyllus impressus, proposing T. subdiminutus as a synonym and providing new data on postcranial bones for this taxon. Tremacyllus specimens from Mendoza reveal a wide and continuous morphological variation that encompasses the morphological differences of species previously considered valid, emphasizing the need for a systematic study focused on all representatives of the genus. We also recognize Paedotherium typicum, which shows a combination of features differing from other species of the genus. The large sample allows us to improve the diagnosis for both the genus Tremacyllus and the species T. impressus and P. typicum. Both species coexist in the Huayquerías Formation; T. impressus is also present in the Tunuyán Formation, whereas the specimens recognized as Paedotherium in this unit were not identifiable at species level. Applying geometric morphometric methods on the dentition, we partially support the taxonomic decisions. We present the first phylogenetic analysis including all the species of Tremacyllus and Paedotherium, using morphological characters of skull and postcranium. According to our results, Tremacyllus is a monophyletic group supported by two synapomorphies, whereas Paedotherium is paraphyletic, in agreement with the prior hypothesis. The record of Paedotherium typicum presented here extends the biochron of this taxon into the late Miocene, which is relevant for establishing biostratigraphic and paleobiogeographic affinities with other Miocene localities.