Acknowledgment of intraspecific variation is an important part of a reliable species diagnosis. For mammalian taxonomy, tooth morphology is an especially important trait and, therefore, the morphological variability of these structures is also greatly significant. Here we describe major dental variation present for Protolipterna ellipsodontoides Cifelli (Litopterna) based on a sample of more than 500 teeth and provide a differential diagnosis distinguishing the species from its sister taxa. Initially, the sample was carefully observed under stereomicroscope in order to identify variable traits. Further variable features were also highlighted by a geometric morphometric analysis. We conducted statistic tests to assess the likelihood that the fossils belong to a single species and the single identity of the sample was recovered. A great deal of our results show that structures like the parastyle, hypocone, conular cristae and ectoflexus can show different degrees of development for the same species. The tooth outline may also show some variation in shape and proportions. Many of those features are used as characters of phylogenies, however, the results obtained indicate these traits to be inappropriate for this sort of study, as they are variable within a single species. Some accessory cusps were also found, but they have very low frequency. Furthermore, these traits lack a clear phylogenetic signal and hence are of dubious validity to taxonomy and systematics.