Shape and age variation in dentition of Paleogene extinct native South American ungulates (Notoungulata) has been traditionally described using qualitative and quantitative approaches, and has played a controversial role in the systematics of several groups. Such is the case of the Notopithecidae, a group of notoungulates with low‐crowned teeth, known from the middle Eocene of Patagonia (Argentina). In this group, as well as in other contemporary families, extreme morphological changes associated to increasing dental wear were originally assumed to represent taxonomic differences; thus, dozens of species were erected, clearly reflecting the difficulty of defining discrete characters. In this contribution, a total of 89 upper molars and 91 lower molars were analyzed distributed in two factors, wear and species; three species of notopithecids were considered as study case, Notopithecus adapinus, Antepithecus brachystephanus, and Transpithecus obtentus, based on the large and well‐identified sample of upper and lower molars for each species. We have coupled geometric morphometric analyses with traditional comparative methods to get a better understanding and interpretation of both the changes in tooth shape contour and the link between shape and ontogeny. In addition, we evaluate the utility of this approach to identify which changes are strictly wear‐related and also test the qualitative characteristics used for diagnosing and differentiating notopithecid species. Our study yielded consistent results when applying independent geometric morphometric analyses on complex structures such as brachydont molar teeth. The landmark data is highly congruent with alternative sources of evidence, such as morphological studies using discrete characters. In notopithecid species, wear is the main factor affecting molar shape, followed by species (in lower molars) and allometry; in addition, lower teeth morphology is more definitive in separating species than upper molars, a fact that entails a key point for systematic studies of Paleogene brachydont notoungulates.Facultad de Ciencias Naturales y Museo