In Japan, wild evergreen azalea species with high ornamental value, such as Rhododendron ripense, grow naturally, and numerous cultivars have been developed based on these species. In this study, we utilized microsatellite markers to examine the genetic relationships among wild evergreen azalea species in Japan, particularly focusing on R. ripense, as well as assessing the genetic diversity of R. ripense. STRUCTURE analysis revealed that when K = 2, R. ripense appeared to be distinct from other species. However, when K = 4, the R. ripense population exhibited two separate clusters. Further analysis at K = 10 revealed genetic diversity within the R. ripense population, which was divided into five clusters reflecting their respective geographic distributions. Analysis of cultivars related to R. ripense based on the results of wild species suggested that most of the Ryūkyū-tsutsuji (R. × mucronatum) cultivars originated from the Yamakuni River in the northern Kyushu region or the San’in region of R. ripense.