Hydrangea luteovenosa is a critically endangered plant species of Jeju Island in Korea, though it is widely distributed in western Japan. We isolated and characterized five microsatellite loci in this species. The number of alleles ranged from 3 to 27, observed heterozygosity from 0.27 to 0.86, and expected heterozygosity from 0.34 to 0.91. The markers described here will be useful for investigating the genetic diversity, genetic structure, and gene flow of H. luteovenosa, and the genetic findings would contribute to the establishment of effective conservation measures for this species in Korea.