Stellera chamaejasme L. is a toxic perennial herb found in open and dry places such as grassland and meadow in Bhutan, Nepal, northern China, Mongol, the Far East Russia, and Korea. Jejudo island population of S. chamaejasme, which is designated as endangered species from 2018. Plant of S. chamaejasme used in traditional Chinese medicine have a potential as a new drug for anti-inflammatory, analgesic, and cutaneous wound healing purposes. To understand the Asia of S. chamaejasme, we develop microsatellite marker. 184 individuals from Jejudo island, Mongolia, Inner Mongolia of China and Yunnan were examined. It also conducted an on-site survey of two areas east of Jejudo island. As a result, the genetic diversity of Jejudo island population was similar to Mongolia and Inner Mongolia of China population. Principal coordinate analysis (PcoA) showed that Jejudo island population is genetically a group of Mongolia and Inner Mongolia of China population and was distinguished from Yunnan of China population. As a result, It has been thought it was introduced during the Mongolian Invasion in 13th century. S. chamaejasme is being threatened with habitat destruction, the spread of invasive species, overharvest from the wild, climate change, population growth and other human activities at present. Our study provide methods for S. chamaejasme conservation and a valuable alternative to plant diversity studies, management of genetic resources.