This paper firstly introduces the concept, method and current research of molecular phylogeography and then discusses its application in the study of geoherbs. The relativity between three genetic differentiation patterns of plant inferred by molecular phylogeography (i.e. allopatric fragmentation, restricted gene flow with isolation by distance and range expansion) and the formation of genuine character is analysed. Molecular authentication of geoherbs based on molecular phylogeography has the advantage of former molecular identification at technology and knowing genetic differentiation of geoherbs. Using molecular phylogeography for study on changing history of geoherbs habitat is also explicated. The problem of germplasm degeneration in cultural geoherbs could be effectively resolved by molecular phylogeography method. The application of molecular phylogeography in these subjects opens up prospects for study on geoherbs by using the principle and method of molecular phylogeography.