Abstract: We compared genetic characteristics of Fagus crenata between natural and planted populations in Saitama Prefecture using chloroplast DNA and nuclear microsatellite（ SSR） markers. In 13 nature populations, most individuals possessed haplotype F, except one individual with haplotype E which is uniquely found so far at areas of the southern part of Nagano Prefecture, the eastern part of Yamanashi Prefecture and the eastern part of Shizuoka Prefecture, and ever not found in Saitama Prefecture. We also detected introduced haplotype B, which is mainly distributed along the Japan Sea side natural populations, but not those in Saitama Prefecture, in three of four planted populations. Seedlings planted those populations were derived from the northern part of Gunma Prefecture where there is heavy snowfall in winter. The genetic diversity of the natural populations tends to be smaller in the order of continuous, belt-like, and the patchy populations, and significant difference was found between the continuous and patchy populations. As to some of patchy populations, a decrease of genetic diversity and the occurrence of inbreeding due to a population size reduction was suggested. The genetic diversity retained within planted populations was approximately equivalent to those of continuous or belt-like populations in Saitama Prefecture. While growth disorder such as dieback is not found among seedlings with the introduced haplotype at the present, genetic disturbance due to the planted trees belonging to genetically different groups might be happed in future. In case of afforestation, planting stocks should be carefully chosen considering the genetic characteristics of the natural forests and planting seedlings.