This study presents the first direct evidence of millet cultivation in Neolithic southeast coastal China. Macroscopic plant remains and phytoliths, together with direct accelerator mass spectrometry (AMS) radiocarbon dates on crops, have shown that both foxtail millet and broomcorn millet were cultivated with rice in the Huangguashan and Pingfengshan sites in Fujian province around 4000-3500 cal. BP. Ratios of different parts of crop remains revealed that crop processing activities such as dehusking and sieving were conducted within the site and thus demonstrated the local production of these crops. The new data, especially the discovery of foxtail millet and broomcorn millet, have greatly changed the current knowledge about the ancient distribution of millet in South China and have now identified southeast China among the potential source-region of Neolithic crops transported overseas to Taiwan and Island Southeast Asia. This study further draws a potential dispersal route of Austronesian languages and people from southern China through Taiwan throughout Southeast Asia.