The species distribution of Fagus crenata, or Japanese beech, in the Japanese archipelago shifted northward during phytogeographical changes that occurred during the Pleistocene and Holocene epochs. Presently, the continuous natural distribution of beech reaches north to the Kuromatsunai-Depression of Hokkaido Island, Japan. In addition, dozens of marginal patches and isolated individuals north of the continuous distribution have been observed. F. crenata grows remarkably well among these small-scattered northern marginal populations, which must have originated from seeds dispersed beyond the northern limit of the continuous beech forest. It is conceivable that the distribution of F. crenata is still in the process of expanding northward. We investigated the genetic structure of 33 beech populations to evaluate the population gene diversity at the leading northern edge of the range expansion. We analyzed 12 nuclear microsatellite loci in each of the 1,693 individuals. Genetic diversity parameters such as expected heterozygosity and allelic richness were clearly lower in the northernmost populations. We found genetic differentiation in the northernmost distribution range (F-ST=0.045, G(ST)'=0.242). STRU CTURE analysis revealed that the southwestern continuous populations consisted of homogeneous ancestral clusters. However, northeastern marginal populations consisted of mixtures of highly differentiated clusters with higher levels of genetic drift than found in the continuous populations.