Analysis of the mitochondrial cytochrome oxidase subunit I sequences of four species of Charybdis crabs reveals genetic differences between them and the phylogenetic affinities among them. In C. affinis and C. japonica, no sequence divergence was observed between samples from Taiwan and the Zhujiang estuary. The two species are closely related but genetically distinct and may represent sibling species. The present result is consistent with results based on morphological and allozyme analyses.