We use high-resolution computed microtomography (micro-CT) and computer-aided tools to examine the 3D changes in the expression of metrical and orphological features at the enamel-dentine junction (EDJ) and at the outer enamel surface (OES) through the complete postcanine dentition of one of the best preserved maxillae and mandible of an early hominin ever found. This specimen (Sts 52) from Sterkfontein, South Africa, represents Australopithecus africanus and is about 2.5 million years old. We also use micro-CTs of a mandibular comparative sample of one common chimpanzee (Pan troglodytes), one pygmy chimpanzee (Pan paniscus) and three extant humans. We find that the 3D-EDJ mandibular metameric pattern observed between the two chimpanzee mandibles is much smaller than the extant human metameric pattern. The 3D-EDJ shape metameric variation in shape is high and complex since the differences within the same species and/or genus can vary from one individual to another and can therefore mask differences between taxa. Importantly, the 3D-EDJ mandibular metameric variation in extant humans can be greater within individuals than between individuals, with differences in shapes appearing larger for Journal of Anatomy For Peer Review Only the M2s than for the M1s. Therefore, we recommend the use of a new paradigm in which between versus within individual metameric variation is systematically assessed on securely identified members of a morphological class, before making inferences about differences between fossil hominin species. The fossil hominin examined in this study - Sts 52 - shows a metameric pattern of mandibular variation in shape which is comparable to the pattern seen between the two chimpanzees. This degree of metameric variation appears relatively small as compared to the much larger patterns of variation observed between extant humans and even within them. We conclude that the distinctive extant human pattern of high 3D-EDJ metameric variation has appeared in a more recent hominin than A. africanus.