This research focuses on an Australopithecus versus Paranthropus comparison using a promising landmark-free morphometric method, which analyzes the shape of two anatomical structures: the endocranium and the enamel-dentine junction (EDJ) on complete dental arcades.Landmark-based approach is often used in morphometry to statistically study shape differences but it involves pointing manually some specific points, which could implicate arbitrary assumptions. We present a method for the generation of 3D anatomical atlases based on landmark-free deformation maps. These statistical atlases are composed not only of an average template but also quantify local morphological variation. They are then used to classify anatomical 3D data. More precisely, an average shape and deformation maps describing how each individual surface differs from the average shape are estimated using "currents", a mathematical model for surfaces, curves, point sets and volume. New specimen can then be classified with deformation comparisons, and the approach permits also to highlight the local variability for each species.Atlases were built with EDJs as well as endocrania from extant human, bonobo and chimpanzee. A linear discriminant analysis using the deformations was significant for identification of extant species both based on endocranium or EDJ. We also determined the taxonomic usefulness of endocrania versus EDJs, and we used the variability of these samples to compare Australopithecus africanus (Sts 5, Sts 52) with Paranthropus robustus (Sk 48, Skw 5). This study gives visual and quantitative tools to study inter and intra-species variability, providing a better model for the comparison and the classification of new fossils.