Halenia corniculata (L.) Cornaz is an endangered species in Korea and distributed in only a few locations, such as Mts. Hwaak and Sorak. Its distribution outside of Korea shows a broad range in cold temperate regions including Mongolia, northeastern China, Russain Far East, and northern Japan, where population size is usually large. To examine genetic diversity of H. corniculata in the Korean population and evaluate the level of genetic differentiation between the Korean and foreign populations, we surveyed 103 candidate SSR motif markers for H. corniculata from sequence data of the amplified fragment with specific length in genome. Among them, 18 genomic-SSR markers were selected to identify group-to-population polymorphism. We collected 17 samples from Mt. Hwaak in Korea, 20 from Hokkaido in Japan, and 20 from Mt. Paektu in China. As a result, a total of 108 alleles corresponding to 104-359 bp was identified. Measuring the type and frequency of alleles observed in each population, the genetic diversity within population was highest in Mt. Hwaak population. Five of 18 loci have unique alleles to the Korean population and can be used as markers to verify the authenticity of Korean Halenia corniculata. AMOVA analysis showed that the Korean population is genetic differentiated from other foreign populations, suggesting that the geographically isolated Korean H. corniculata is genetically diverged.