In the present study, we assessed the inter- and intrapopulation genetic and morphological variation of Cerithidea decollata along the eastern coast of Africa. The population structure of C. decollata along the latitudinal gradient was examined by sequencing 420 bp of the mitochondrial cytochrome c oxidase I (COI) gene in 172 snails from 29 sites, in a combined analysis with geometric morphometrics in 1799 snails from 32 sites. Analysis of molecular variance and spatial analysis of molecular variance showed a moderate spatial population differentiation from Kenya to the Republic of South Africa, suggesting genetic divergence between the northern, central, and southern regions. This structure appears to be the result of life-history traits combined with oceanographic features. Haplotype network and mismatch analysis suggest a recent population expansion during the Holsteinian interglacial period in the northern region and several colonization events in the central and southern regions. The morphometric approach suggests that morphological variation in shell shape is somewhat independent of the genetic divergence, revealing an overlap of shape across the latitudinal gradient but significant differences among-population at a local level. This may indicate that similar ecological pressures are acting along the coast, leading to the occurrence of similar morphological characters. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107, 647–663.