Vestimentiferan tube worms (Annelida: Siboglinidae) were discovered in a hydrothermal field at a depth of 195 m in the crater of the submarine volcano Omuro Dashi in the Izu-Ogasawara Arc. Based on the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene in individuals sampled in 2022, they were identified as Lamellibrachia satsuma Miura, Tsukahara & Hashimoto, 1997. STRUCTURE analysis and discriminant analysis of principal components (DAPC) based on 14 microsatellite markers showed a large genetic deviation of the population of Omuro Dashi from those of Kagoshima Bay and the north Mariana Arc (the Nikko and Daikoku Seamounts), whereas the population of Omuro Dashi did not show significant genetic deviation from that of the Nikko Seamount based on the COI gene. All analyses showed that individuals of a methane seep area on the Kanasu-No-Se Bank, the Nankai Trough, which were collected only in 1994, were more closely related to those of Omuro Dashi than to those of other habitats. These results suggest that the ancestors of the Omuro Dashi and Nankai Trough populations originated from migrants from the north Mariana Arc and that there might be undiscovered source population(s) of L. satsuma around the Nankai Trough.