We present a dated phylogeny for all species of Coptis, a genus of pharmaceutical and economical importance. Our biogeographical inference indicates that a vicariance event between Japan-western North America and eastern North America occurred in the Middle Miocene, resulting in the split of Coptis and Xanthorhiza. The most recent common ancestor of Coptis occurred in western North America, southern East Asia and Japan. In Coptis, two vicariance episodes, involving Japan and western North America-southern East Asian and western North America and southern East Asian, took place at ca. 9.55 Ma and 7.78 Ma, respectively. Two dispersal events happened from mainland Asia to Japan at ca. 4.85 Ma and from Japan to Taiwan at ca. 1.34 Ma, respectively. This study shed light on the past floristic exchanges between East Asia and North America, as well as within East Asia.