Tooth crown morphology plays a central role in hominin systematics, but the removal of the original outer enamel surface by dental attrition often eliminates from consideration the type of detailed crown morphology that has been shown to discriminate among hominin taxa. This reduces the size of samples available for study. The enamel-dentine junction (EDJ) is the developmental precursor and primary contributor to the morphology of the unworn outer enamel surface, and its morphology is only affected after considerable attrition. In this paper, we explore whether the form of the EDJ can be used to distinguish between the mandibular molars of two southern African fossil hominins: Paranthropus (or Australopithecus) robustus and Australopithecus africanus. After micro-computed tomographic scanning the molar sample, we made high-resolution images of the EDJ and used geometric morphometrics to compare EDJ shape differences between species, in addition to documenting metameric variation along the molar row within each species. Landmarks were collected along the marginal ridge that runs between adjacent dentine horns and around the circumference of the cervix. Our results suggest that the morphology of the EDJ can distinguish lower molars of these southern African hominins, and it can discriminate first, second, and third molars within each taxon. These results confirm previous findings that the EDJ preserves taxonomically valuable shape information in worn teeth. Mean differences in EDJ shape, in particular dentine horn height, crown height, and cervix shape, are more marked between adjacent molars within each taxon than for the same molar between the two taxa.