The phylogenetic relationships were analysed based on nucleotide sequences of a mitochondrial gene for cytochrome c oxidase subunit I (COI) for the vestimentiferan tube worm Lamellibrachia juni, which inhabits three extremely acidic hydrothermal vent fields in the South Pacific: the TOTO Caldera in the South Mariana Volcanic Arc, the DESMOS site in the Manus Basin, and the Brothers Caldera in the Kermadec Arc. Six haplotypes were obtained from 34 lamellibrachiids from the three sites. Each haplotype was obtained only from a single site, which suggests that the three populations have been isolated from each other. Haplotypes from the DESMOS site formed a monophyletic cluster. All ten individuals from the TOTO Caldera were classified into the same haplotype, which was shown to form a monophyletic cluster with one of three haplotypes from the Brothers Caldera. The population in the Brothers Caldera was shown to consist of two genetically distinct groups.