We have investigated the genetic diversity, genetic components, and genetic relationships among the Fagus crenata natural populations that are used as seed stands, and the seedlings derived therefrom in Niigata and Yamanashi Prefectures, by using nuclear microsatellite markers. Seedlings showing almost the same level of genetic diversity as that of the related seed stand populations have been produced in Niigata Prefecture. Although the value of allelic richness in the Yamanakako seedling population in Yamanashi Prefecture was lower than its seed stand population, the value of heterozygosity was comparable. STRUCTURE analysis revealed that the seedling populations in Tsunan, Takigashira and Yasuda in Niigata Prefecture, and Yamanakako showed differences in the ratio of each cluster from the related seed stand populations, suggesting a possibly different genetic composition between them. In particular, the relatedness among individuals in the seedling population of Yamanakako was higher than that in its seed stand population. The possible impacts of seeds from limited mother trees were also considered. The results of this study suggest that the current methods of seed collection have almost no problems relative to maintaining genetic diversity, but the number of mother trees and/or seed collecting sites should be increased in order to maintain genetic compositions similar to those found in natural forests in these regions.