Nucleotide sequence data of the mitochondrial cytochrome oxidase I (COI) gene, were compared among 17 specimens of Sacculina carcini parasitising three portunid hosts as a preliminary assessment of haplotype structure in a poorly understood species for which there are few morphological characters on which to base taxonomic analysis. S. carcini parasitising Carcinus maenas (from Sweden, England and Denmark) were compared with S. carcini parasitising Liocarcinus marmoreus (from Ireland) and Liocarcinus holsatus (from Wales). Specimens of three congeneric sacculinid species and one confamilial species were included in the comparison as outgroups. The comparison confirmed that specimens of S. carcini from different hosts and different regions are all the same species. The data also suggested geographically consistent sequence differences among sampled sites, high levels of similarity within sites and very large differences between species, all of which suggests that analysis of the COI gene sequence could be a useful method for resolving population genetics and taxonomy of rhizocephalans.