Background: Deep-sea hydrothermal vents are dynamic environments with exotic faunas. In this study, we found a new species of Branchipolynoe (Aphroditiformia: Polynoidae) polynoid scale worm living in the recently discovered mussel Gigantidas vrijenhoeki in deep-sea hydrothermal vents and methane seeps at depths of 2,014 - 2,023 m. Associations between scale worms and giant mussels are common in hydrothermal ecosystems.Results: We analyzed the morphology of Branchipolynoe from the Onnuri vent field (OVF) on the northern Central Indian Ridge and sequenced the full mitochondrial genome. Based on its morphological traits and mitochondrial genes, we designated the specimens as Branchipolynoe onnuriensis n. sp., described herein. This species resembles B. longqiensis and B. tjiasmantoi, but is distinguished by its notopodial acicular lobe form and the tips of the subacicular neurochaetae. The identity of the new species was well supported by genetic distance and phylogenetic analyses of the mitochondrial c oxidase subunit I (COI) gene. Genetically, the new species is closest to the Western Pacific species B. tjiasmantoi; phylogenetic analyses support the correlation between Indian Ocean and Western Pacific hydrothermal polychaetes. This study provides a foundation for exploring the evolutionary relationship between scale worms and giant mussels.