This paper summarises the results of 225 studies of seed impressions in pottery assemblages from 182 archaeological sites across Kyushu, Shikoku and Honshu islands covering the Late/Final Jomon–Middle Yayoi period (ca. 2000–1 BCE). Focussing on rice, foxtail millet and broomcorn millet impressions, this archaeobotanical dataset was used to reconstruct when and where these crops arrived from the Eurasian mainland on these islands, how they dispersed and whether there were changes in crop preferences over time. While it is generally accepted that crop cultivation started during the Initial Yayoi period (ca. 800/700–500/400 BCE) in northern Kyushu, a limited number of seed impressions in Tottaimon phase 1 pottery suggests that rice and millet were present at different sites on Kyushu and in the Chugoku region even before this period. The earliest impression records also corroborate the hypothesis that rice arrived along with both millet crops, which for a long time have not been considered in research on early agriculture. The earliest crop records from eastern Japan (here Central Highlands to northern Honshu) come from early Fusenmon pottery, which was mainly used in the Central Highlands (central Honshu) and some adjacent areas, dating to the End of Final Jomon period (concurrent with the Initial Yayoi period in northern Kyushu). While the records from western Japan (here Kyushu to Kinki region) associated with Tottaimon pottery suggest mixed rice/millet cultivation during the Initial Yayoi and early part of the Early Yayoi (ca. 800/700–300 BCE) period, Fusenmon groups appear to have preferred millet. In western Japan, related to the spread of Ongagawa pottery, rice became the dominant crop during the late Early Yayoi period. This shift happened later (i.e., during the Middle Yayoi period; ca. 300–1 BCE) in eastern Japan. This ‘delay’ is manifested in impression records from the Tokai region representing a transitional area between eastern and western Japan. Rice-centred agriculture begun with the arrival of Ongagawa pottery on the Nobi Plain during the Early Yayoi period. In regions east of the plain settled by Jokonmon pottery groups a more rice-oriented agriculture is not evident before the Middle Yayoi period. An exceptional development is indicated for northern Tohoku (northernmost Honshu). Impression records from Sunazawa pottery suggest that local groups adopted only rice during the Early Yayoi period. The rice preference apparently continued into the Middle Yayoi period, but crop cultivation was abandoned by the beginning of the Late Yayoi period.
