The paper introduces the current situation and the characteristics of the medicinal plant core collection. It expounds the significance and research methods for the medicinal plant core collection based on molecular phylogeography. Guided by molecular phylogeography, the essay explores the feasibility and methods of medicinal plant core collection for the medicinal plants with rich wild resources and without wild resources. It further forecasts the application of medicinal plant core collection methods on the basis of molecular phylogegraphy.