This project provides transcriptome sequencing data of two deep-sea bathymodiolus mussels (B. platiforns and B. manusensis, which are sampled from a cold seep at the South China Sea and a vent at Manus respectively) and their coastal relative Modiolus kurilensis mussels (sampled from Xiaoping island at Dalian, China). The primary goal of this study was to provide an outline on the genetic basis for the adaptations of mussels in diverse habitats and mainly focused on deep sea mussels, as well as figure out genetic features that fasten the linkage between the deep-sea mussels and their endosymbionts. The work will extend our understanding on the mechanism that survives deep-sea mussels from the harsh environments.