Hydrangea lutovenosa is a deciduous shrub that grows on the forest floor of temperate forests in western Japan and Jeju Island of Korea. Although it is common in Japan, H. lutovenosa is considered as a critically endangered plant species of Korea with a noticeably small size population. We investigated current status of H. luteovenosa in Korea, with emphasis on its genetic diversity. Only one population had been known in Jeju Island, and we found the population was consist of 285 individuals. All individuals were mapped and measured the size of the tallest stem. Plant sizes in the Korean population were significantly smaller than Japanese plants. All individuals were genotyped with nuclear microsatellite markers developed for this study. Three Japanese populations were also investigated and genotyped for comparative analyses. The result of genotyping showed that the Korean population has extremely lower genetic diversity, and only one clone had been found so far. This result suggests that the current Korean population has been maintained mostly by vegetative reproduction.