The Saururus chinensis (Lour.) Baill. is a perennial herb which is widely distributed in China, India, Japan, Korea, the Philippines, and Vietnam. However, the distribution of this species in South Korea is restricted to lowlands of eastern areas in the Jeju Island. Also, this species has been threatened from the illegal collections and indiscriminate development. Consequently, S. chinensis has been designated as an endangered species by the Ministry of Environment. We isolated and characterized microsatellite loci of S. chinensis by using NGS method. A total of 15 microsatellite loci were developed and tested in Korean, Japanese and Chinese populations. The number of alleles per locus varied from two to six. The observed and expected heterozygosities were 0.000 to 1.000 and 0.056 to 0.564, respectively. A total of 3 loci (site 1), 4 loci (site 2) in the Korean population, 5 loci in the Japanese population and 5 loci in the Chinese population deviated from Hardy-Weinberg equilibrium. We are now performing population genetic analysis of approximately 500 individuals from 20 populations, reflecting their geographic distributions. We expect that these newly developed microsatellite markers will contribute to understanding current S. chinensis distributions and relationships between the populations to prepare conservation strategies.