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We sequenced the mitochondrial ND4 gene to elucidate the evolutionary processes of Bathymodiolus mussels and mytilid relatives. Mussels of the subfamily Bathymodiolinae from vents and seeps belonged to 3 groups and mytilid relatives from sunken wood and whale carcasses assumed the outgroup positions to bathymodioline mussels. Shallow water mytilid mussels were positioned more distantly relative to the vent/seep mussels, indicating an evolutionary transition from shallow to deep sea via sunken wood and whale carcasses. Bathymodiolus platifrons is distributed in the seeps and vents, which are approximately 1500 km away. There was no significant genetic differentiation between the populations. There existed high gene flow between B. septemdierum and B. brevior and low but not negligible gene flow between B. marisindicus and B. septemdierum or B. brevior, although their habitats are 5000–10 …