We studied and compared genetic variation of Korean pine (Pinus koraiensis Sieb. et Zucc.) from 12 natural populations in Korea, China, and Russian Far East using allozymes and random amplified polymorphic DNAs (RAPDs). Eighteen polymorphic allozyme loci and 38 polymorphic RAPD fragments were analyzed. The level of allozyme diversity (A = 1.95, P95 = 46.8%, Ho = 0.158, He = 0.169) and the degree of genetic differentiation (FST = 0.069) were comparable to those of other pines with similar life histories and ecological traits. Allozyme (He) as well as RAPD (Shannon’s index) variation decreased from south (Korea) to north (Russia), providing an evidence for the hypothesis of Korean pine’s northward migration. Differentiations among three different regions (Korea, China, and Russia) as well as among populations within regions were small. Substantial gene flow (Nm = 3.4) may be a partial explanation to this result. Clustering algorithms using various genetic distance measures showed some decisive geographic patterns at allozyme and RAPD level: the geographically close populations tended to be clustered together. On the other hand, two Chinese populations, Xobukho and Wangging, were grouped with the Russian populations rather than with the other Chinese populations. The Xiaoxing’anling and other mountains extended from north to south seemed to function as a barrier against gene flow between the Xobukho and Wangging (located east of the mountains) and the other Chinese P. koraiensis populations (located west of the mountains). The genetic diversities and differentiation estimated from RAPD data in Korean pine were congruent with those of allozymes.