The archaeology of the Jomon and other prehistoric periods currently faces a major turning point. This is evidenced by the fact that the results of conventional archaeological work have often been significantly modified by the results of physical and chemical analyses. It has become extremely difficult to approach the real image of the past only by archaeological methods, and in order for the archaeology of the prehistoric period to develop in the future, archaeology itself needs to shift from its traditional humanities-based area and be reborn as a new academic field. In this research field, we propose the establishment of an integrative bioarchaeology that combines current archaeological methods with natural science approach such as dating, isotope analysis, and genome analysis, focusing mainly on excavated materials such as human bones, animal and plant remains, in Japan.