Polynoid scale-worms invaded the deep-sea around 60 million years ago, and are currently a group of common invertebrates in deep-sea chemosynthesis-based habitats. We aimed to gain insights into the adaptation and evolution of deep-sea scale-worms by comparing the transcriptome of Branchipolynoe pettiboneae (a species living in the mantle cavity of deep-sea mussels in hydrothermal vents and cold seeps), Lepidonotopodium sp. (a free-living deep-sea species in hydrothermal vents), and Harmothoe imbricata (a shallow-water species).