I-SSR variants were analyzed to estimate level and distribution of genetic diversity in 19 populations of Japanese red pine in Korea (10 populations), China (6 populations), and Russia (3 populations). A total of 66 I-SSR variants were observed in the analyzed 551 individuals. All the analyzed individuals could be identified by DNA fingerprints-like individual specific amplicon profiles. Relatively higher level of genetic diversity within populations was observed in 19 populations of Japanese red pine (mean of 0.396) than other tree species. From the results of AMOVA with all 19 populations, relatively high degree of genetic differentiation ( ST=0.199) was allocated among populations although majority of genetic diversity was distributed within populations (80.01%), After dividing 19 populations into 3 geographic groups, the degree of population differentiation within groups was lowered to 0.153. The degree of population differentiation was decreased more to ST=0.135 by including only 10 Korean populations. Genetic relationships among 19 populations, reconstructed by UPGMA method, revealed 2 weak genetic groups. Three Russian populations were grouped with the most distantly located Chinese population of Xu Gou instead of 2 closely located Chinese populations of Mu Dan Jiang and Long Jing. The overall genetic relationships among the 19 populations were not coincided with geographic affinity. The discrepancy between genetic relationships and geographical distribution among the populations suggested that the analyzed populations might be undergone random changes in genetic composition. The probable cause of the random changes was discussed. PCR-RFLP analyses of mtDNA revealed no variation among 57 individuals selected from 19 populations. Results obtained in this study suggested that more careful approach should be made for preparing strategy for gene conservation of Japanese red pine in Korea, China, and Russia.