Significance: Palaeoecological analysis reveals that the expansion of rice agriculture in southern China and Southeast Asia around 2,000 y ago caused widespread deforestation and biodiversity changes in tropical and subtropical forests. Tropical forests, with the highest level of plant diversity and concentration of endemic species, suffered greater decline of arboreal richness than forests in subtropical and temperate areas. In subtropical ecosystems, total plant richness increased, despite arboreal decline, possibly thanks to the flourishing of herbs in an opening landscape. The disappearance of Glyptostrobus in southeastern Asia provides a case study as to how early rice agriculture endangered an endemic species by causing losses of its natural habitats, with prehistoric land-use changes leaving a clear legacy for today’s landscapes and species compositions.