Lonicera caerulea var. edulis is a rare species found in some alpine region of Korea. Genetic variation in L. caerulea var. edulis has been investigated by examining 161 individuals from six natural populations: Mt. Seorak 1, Mt. Seorak 2, Mt. Jeombong, Mt. Bangtae, Mt. Gyebang, Mt. Halla. The mean genetic diversity for all the six populations was 0.25 (S.I.). The highest genetic diversity was found in Mt. Seorak (S.I.=0.3158) and the lowest was in Mt. Gyebang (S.I.=0.1047). Comparatively low level of genetic diversity was observed (Ae=1.25, P= 64.6%, S.I.=0.25), which is a typical pattern for rare tree species. AMOVA showed exceptionally large proportion of genetic variations both for among populations (34.69%) and within populations (65.31%). Excluding Mt. Gyebang, the genetic variation among and within population was 18.71% and 81.29% respectively. The UPGMA dendrogram based on genetic distance is not suitable for geographic relationship. Genetic distance of Mt. Gyebang was most distant from the other populations. Excluding Mt. Gyebang, the genetic identities among the five populations were 0.95 to 0.97, which is very high similarity level of genetic identity. This low level of genetic variations and the lack of site in nature indicates that L. caerulea var. edulis demanded a serious conservation.