Species of hermit crabs in the genus Clibanarius Dana, 1852 have adapted to various environments in the intertidal areas, including hard substrates and soft sediments. These species often bear a close morphological resemblance to each other, therefore, the colouration on the pereopods can be one of the reliable characteristics to distinguish the species. However, the evolutionary relationships among species with different colour patterns and relationships between colour patterns and habitat adaptation have not previously been investigated. Therefore, we reconstructed the phylogenetic relationships among 19 species of Clibanarius based on mitochondrial [12S rRNA, 16S rRNA and cytochrome oxidase I] and nuclear [histone H3] DNA markers. The results suggest that the striped and solid colour elements have evolved multiple times independently, with the ancestral colour pattern potentially being scattered, bright colour spots with a bright colour band. Our findings also suggest that evolutionary adaptation from hard substrates to mudflats and soft sediments may have occurred at least twice.