<p><i>Rhododendron sohayakiense</i> var. <i>koreanum</i> is a shrub belonging to the Ericaceae family, found on the rocky summits of mountains above 1,000&#xa0;m in the southern part of the Korean Peninsula. As a subalpine plant, it is vulnerable to the effects of climate change, making it a priority species for monitoring. This study was conducted to conserve and manage the genetic diversity of <i>R. sohayakiense</i> var. <i>koreanum</i>. A total of 270 individuals from 8 populations across its range were analyzed using 11 microsatellite markers. The mean observed heterozygosity (<i>H</i>_<i>o</i>) was 0.486, the mean expected heterozygosity (<i>H</i>_<i>e</i>) was 0.538, and the differentiation among populations (<i>F</i>_<i>ST</i>) was 0.248. The genetic diversity of the populations was similar to plants vulnerable to climate change, and due to their isolated distribution and insect pollination, genetic differentiation among populations was high. Bayesian clustering showed that the 8 populations were grouped into 4 clusters, and this result was also supported by Principal coordinates analysis (PCoA) and a UPGMA dendrogram. Considering the clustering results and the genetic diversity of each population, Mt. Baegun and Mt. Sambong were selected as in situ conservation populations. The estimated effective population sizes of two selected populations are 43 and 17, respectively, which are fewer than the minimum population size (50) required to prevent inbreeding. Therefore, Forest Genetic Resource Reserves should be established to preserve as many native <i>R. sohayakiense</i> var. <i>koreanum</i> as possible in each region to avoid reducing the effective population size and inbreeding. Moreover, a genetic diversity monitoring strategy was proposed by considering peak units based on the distance between genetically similar individuals.</p>