The genetic structure and morphometric differentiation of mangrove crab Perisesarma guttatum populations were examined among shelf connected locations along a latitudinal gradient on the East African coast. Over 2200 specimens were sampled from 23 mangrove sites for geometric morphometrics analysis. Population genetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences were used to evaluate connectivity among populations. A total of 73 haplotypes were detected, and almost no haplotypes were found in common between two highly supported phylogeographic clades: southern Mozambique (Inhaca Island and Maputo Bay) and a northern clade that included north Mozambique, Tanzania and Kenya. These two clades were identified based on the species' populations pairwise genetic differentiation and geographical location. ΦST values were considerably high between the two clades, indicating the presence of significant population genetic structure between Kenya and South Mozambique. However, each clade was composed of genetically similar populations along the latitudinal gradient, and no significant population structure was found within each clade because the Φst values were not significant. The morphometric analysis corroborated the division into two clades (i.e. Inhaca Island/Maputo Bay and northern populations) and also detected less shape variation among populations that were few kilometres apart. The significant spatial genetic structuring between the southern and the northern populations of P. guttatum along the geographic gradient under study, combined with morphological differences, suggests that these populations may be considered as cryptic species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 28–46.