In this study, we sequenced plastid DNA to investigate the interspecific relationships of Stemona species. In total, 34 individuals from 23 populations were studied, covering the geographical range of Stemona in China plus eight individuals from Indonesia. Our results show that seven Stemona species cluster into three major clades; S. parviflora is closest to S. javanica of the species studied; it is reasonable to treat S. shandongensis as a synonym of S. sessilifolia, whereas S. japonica is close to S. sessilifolia; the geographically widespread species S. tuberosa possesses a high degree of differentiation and contains three subgroups.