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Based on chronological and archaeobotanical studies of 15 Neolithic and Bronze Age sites from the northern Chinese Loess Plateau and southern Inner Mongolia-the agro-pastoral zone of China-we document changes in the agricultural system over time. The results show that wheat and rice were not the major crops of the ancient agricultural systems in these areas, since their remains are rarely recovered, and that millet cultivation was dominant. Millet agriculture increased substantially from 3000 BC-2000 BC, and foxtail millet evidently comprised a high proportion of the cultivated crop plants during this period. In addition, as the human population increased from the Yangshao to the Longshan periods, the length and width of common millet seeds increased by 20-30%. This demonstrates the co-evolution of both plants and the human population in the region. Overall, our results reveal a complex agricultural-gardening system based on the cultivation of common millet, foxtail millet, soybeans and fruit trees, indicating a high food diversity and selectivity of the human population.