Wikstroemia ganpi grow the southern coastal regions in Korea, small population and are classified as a critically endangered species. The majority of habitats are located near forest paths and reservoirs at the edge of mountains, indicating that there is considerable human interference and severe fragmentation of populations, as well as damage to individuals as a result of forest fires and soil erosion. We evaluated the genetic diversity in populations, genetic differentiation between populations, and genetic structure to provide data to support the conservation of W. ganpi. W. ganpi populations showed lower genetic diversity(mean level: P.95=36%, S.I=0.170, h=0.113) and higher genetic differentiation(40%) between populations than other species with similar characteristics did. And the among population gene flow(Nm) was highly restricted at 0.87. The four populations revealed that there were fixed alleles in the different loci of each population. This result can be explained by the effects of genetic drift. Structure analysis and the PCA results were more indicative of separate groups than a genetic structure that was linked to populations. This reflects the high level of genetic differentiation between populations and the unique alleles within each population. As a result, lower genetic diversity and higher genetic differentiation between populations of W. ganpi. And the effects of inbreeding were observed, as well as asexual reproduction in some populations. Therefore, to conserve W. ganpi, all the surveyed populations need to be designated for on-site conservation and monitored continually. A research on the spatial genetic structure needs to be conducted to obtain information on sample extraction for off-site conservation. This structure would be able to minimize the wasting of samples that could be obtained from limited genetic resources and would enable further focused and efficient management.