Pinus densiflora is a widespread montane conifer that ranges from Japan to Manchuria via Korea. Enzyme electrophoresis was employed to assess genetic diversity and divergence in the populations of the species. Fourteen of the 19 loci (74.0%) were polymorphic in at least one of the 20 populations. Genetic diversity at the species level (Hes) and at the populations level (Hep) were 0.232 and 0.147, respectively. The proportion of total genetic diversity due to difference among populations (GST) was 0.279. An indirect estimate of gene flow (Nm = 0.65) indicates genetic drift is not seemed to play a major role in shaping genetic structure. P. densiflora maintains as much or perhaps more variation with their populations than other tree species in temperate regions.