Coptis chinensis Franch is a very famous traditional Chinese medicinal plant, which was first published in the Shennong Bencao Jing (Divine Farmer’s Classic of Materia Medica) and recorded in dozens of ancient prescription lists such as Jufang and Shanghanlun. Recently, the decoding of Coptis chinensis genome has provided a new opportunity to understand its genome evolution, especially the early evolutionary history of eudicots.