Seriola quinqueradiata (yellowtail) is the most produced and economically important aquaculture fish species in Japan. Although the technologies of yellowtail aquaculture have been improving until now, several issues for the sustainable farming of this species remain to be solved. The increasing of feed cost is a major issue, because the price of fish meal used for yellowtail feeds continues to rise. To develop cost-effective feeds for yellowtail, elucidation of digestive pathways and nutritional requirements of yellowtail is required. In this study, we conducted a RNA-Seq analysis of the digestive organs of yellowtail.