The deep-mussel Bathymodiolus septemdierum is distributed in hydrothermal vents in the Izu-Ogasawara Island-arc, Japan, owing its biomass to the functional dependence on its symbiotic association with chemoautotrophic sulfur-oxidizing bacteria. Little is known about physiological characteristics and ecological significance of endosymbionts. We therefore performed the genome analysis on the endosymbiont of Bathymodiolus septemdierum. The complete genome sequence and comparative genome analysis among sulfur-oxidizing endosymbionts will provide important insights into their evolution, physiological functions, and interactions with their host animals.