For almost a century after E.S. Morse's 1877 excavations at Ōmori shell mound demonstrated the existence of a Stone Age culture in the archipelago, it was generally accepted that the Japanese people dated back only to the Yayoi period, the time when wet-rice farming was introduced from the continent. The Stone Age was associated with pre-Japanese peoples such as the Ainu. By the 1980s, however, the idea that the Stone Age Jōmon period formed a key component in Japanese culture became widely accepted in both academia and the popular imagination. ‘Jōmon’ became a household word for the first time. This essay uses recent interdisciplinary work in archaeology, linguistics and genetics to re-evaluate the contribution of the Jōmon to Japan. New genetic research has started to find significant Jōmon ancestry in ancient Korea, showing that Jōmon genomes were not limited to the Japanese archipelago. DNA studies have also concluded that Yayoi, Kofun and modern ‘mainland’ Japanese populations derive only around 10% of their ancestry from the Jōmon, a figure which rises to 25% for early modern and contemporary Okinawans. Such figures are comparable to reported levels of hunter-gatherer ancestry found in many European countries. Linguistically, with the exception of Ainuic in the north, Jōmon languages were replaced by the incoming Japonic family with, at best, limited borrowing. The idea that Jōmon culture has been a dominant factor in shaping modern Japan also requires reconsideration. Many ‘Jōmony’ traits in historic Japan reflect ecological constraints—there are only so many ways to eat an acorn. Other such traits can be seen as part of a transcultural strategic resistance to Japan rather than as unchanging tradition. While the Jōmon has proven a fecund source of ideology in post war Japan, its actual contribution to historic Japanese civilisation has been small. This conclusion requires a reevaluation of why the Ainu in Hokkaido were not absorbed in the same way as Jōmon cultures elsewhere and why they went on to make such an important contribution to the history of the northern archipelago.