Genetic divergences among populations of Aegla longirostri suggest that this group may be formed by cryptic species. In this study, we analysed the carapace shape of six populations of A. longirostri from southern Brazil, using a geometric morphometric approach, to better elucidate the species' systematics. Our results were congruent with the genetic data, meaning that genetically differentiated populations were also morphogeometrically differentiated. The geometric morphometric descriptors showed significant differences in carapace shape among all populations. Geographical distance and isolation may be affecting the gene flow between populations, leading to divergence in both genetic and morphometric traits. Our data indicate the possible existence of cryptic species within A. longirostri, or an incomplete process of speciation. Geometric morphometric methods were efficient in differentiating among populations that do not show divergence in diagnostic characters. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 31–39.