Marine organisms often show high levels of morphological variation within and among species as a result of adaptation to the habitat heterogeneity in coastal environments. We investigated the relationship between the geographical patterns of two contrasting shell-surface morphotypes (smooth vs ribbed) and genetic diversity in East Asian members of the marine gastropod genus Tegula. We also investigated the geographical and genetic patterns of two shell-colour morphotypes (black vs light brown) in Tegula xanthostigma. We sequenced the mitochondrial cytochrome c oxidase subunit I gene and the nuclear 28S rRNA region, and performed phylogenetic analyses and species delimitation tests. Two morphotypes, distinguished by different sculpture, appeared sympatrically or allopatrically in several ESUs, but could not be distinguished genetically. In addition, although the black morphotype of T. xanthostigma (a smooth-shelled species) and individuals of T. argyrostoma (a ribbed species) have been traditionally classified as separate species, the inferred phylogeny suggests that they belong in same clade and ESU. We also conducted a statistical analysis to determine whether shell morphology (colour or sculpture) varies with the degree of coastal exposure. We found no association between exposure and surface morphology. However, in T. xanthostigma the light brown morphotype preferred sheltered sites when compared with the black morphotype. Molecular methods and statistical analyses showed that smooth T. xanthostigma were divided into two species, with shell colour and habitat preference differing among species. While our findings show that shell sculpture is not a reliable character to use for species delimitation in Tegula, they suggest that differences in habitat preferences may potentially drive the genetic divergences seen in this group.