BackgroundArchaeobotanical remains of millet were found at the Nan-kuan-li East site in Tainan Science Park, southern Taiwan. This site, dated around 5000–4300 BP, is characterized by remains of the Tapenkeng culture, the earliest Neolithic culture found so far in Taiwan. A large number of millet-like carbonized and charred seeds with varied sizes and shapes were unearthed from the site by the flotation method. Since no millet grain was ever found archaeologically in Taiwan previously, this discovery is of great importance and significance. This paper is in an attempt to further analyze these plant remains for a clearer understanding of the agricultural practice of the ancient inhabitants of the Nan-kuan-li East site.ResultWe used light and scanning electron microscopy to examine the morphological features of some modern domesticated and unearthed seeds to compare and identify the archaeobotanical remains by three criteria: caryopsis shape, embryo notch, and morphology of lemma and palea. We also developed a new methodology for distinguishing the excavated foxtail and broomcorn millet seeds.ConclusionTwo domesticated millet, including broomcorn millet (Panicum miliaceum) and foxtail millet (Setaria italica), as well as one wild millet species, yellow foxtail (Setaria glauca), were identified in the unearthed seeds. Together with the millet remains, rice was also cultivated in the area. Archaeological evidence shows that millet and rice farming may have been important food sources for people living about 5000 years ago in southern Taiwan.