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Pachyrukhinae (Hegetotheriidae, Notoungulata) is a highly frequent clade in the Late Miocene-Pliocene outcrops of southern South America. In Argentina, two genera have been recognized for this span: Tremacyllus Ameghino, 1891 and Paedotherium Burmeister, 1888. The simplified ­euhypsodont dentition of these Neogene forms creates significant difficulties when cheek teeth are described for systematic purposes. Tremacyllus has been scarcely studied in comparison with Paedotherium, and taxonomic analyses have interpreted diagnostic features as intraspecific variations and proposed the monospecific status of the genus. Given the discussion regarding the validity of Tremacyllus species and the fact that dental elements are the most abundant remains in the fossil record, we employed a quantitative framework provided by geometric morphometrics and multivariate statistics to discriminating intra- from interspecific variability by tooth outline. We analyzed a large sample of 82 specimens and two hypotheses were tested: 1) there are morphological gaps within the analyzed sample; and 2) morphology follows a pattern of geographical variation within the sample, suitable for recognition of species. We found that morphological variability is organized into two clusters. Morphological gaps are associated with geographical patterns in the P4 and upper premolars datasets. Based on the classification of the type specimens and supported cluster structure, we recognize Tremacyllus incipiens Rovereto, 1914 as a valid taxon, endemic from western outcrops of Northwestern Argentina. Segregation between northern and southern morphologies agrees with two different palaeo-phytogeographic provinces. This approach proved to be very effective to address intra- and interspecific variation and contribute to the knowledge of available techniques to assess morphological variation.