Mussels belonging to the genus Bathymodiolus are frequently found in chemosynthetic ecosystems as dominant animal species and harbor thiotrophs and/or methanotrophs as endosymbionts in specialized cells of gill tissues called bacteriocytes. Although Bathymodiolus species are considered to largely depend on these endosymbionts for nutrition, our knowledge regarding the trophic relationships between these host mussels and bacterial endosymbionts is very limited. For example, cholesterol is a major sterol end product in animals, and probably originate from thermogenic methane seeping up from the sediment. it was suggested that the host mussel utilizes a sterol intermediate compound that is relatively rich in the gill tissues, which may be synthesized by the methanotrophic endosymbionts. It is reasonable to assume that cholesterol biosynthesis in methanotroph-bearing Bathymodiolus could be more precisely understood by comprehensively identifying the genes associated with this synthetic pathway from both host and endosymbionts. First, we carried out transcriptome sequencing of Bathymodiolus platifrons collected at methane seep sites in Sagami Bay, Japan.