Current status of Euchresta japonica in Korea was investigated, with emphasis on its genetic diversity. From field surveys, we obtained the only locality record for the wild population with eight individuals. Genotyping was performed using nine microsatellite markers for all 20 remnants including ex situ collections. Genetic status characterizing the Korean E. japonica is summarized as follow: 1) among nine loci, five show polymorphism with low heterizygosities; 2) Korean population is distinguished from the previously reported Japanese population showing different alleles and higher diversity; 3) a total of 12 multilocus genotypes are detected; 4) among the 20 individuals, two and six individuals have wild and ex situ specific alleles, respectively, and five are proved to have individual specific alleles. In conclusion, we identified genetically critical individuals which can be defined as an individual having population or individual specific alleles. The selected critical individuals should be a top priority for conservation, and will be necessary for the maintenance and recovery of genetic diversity in or ex situ populations of E. japonica in Korea.