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Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) sequences of samples from its distribution range revealed 3 genetically differentiated clades: the South China Sea, Indo-Malay and Taiwan clades. The clades have an allopatric distribution and differed by~ 7.5 to 14% in COI. They also differed in zonation patterns and abundances within vertical ranges. The genetic and ecological differences suggest that the 3 clades probably represent distinct species. There were signatures of postglacial demographic expansion, yet the timing of expansion varied among clades, which is attributable to the differences in their geographical distributions. The Indian Ocean population of the Indo-Malay clade apparently attained its present range by postglacial re-colonization from the Pacific and, as a result …