The genetic lineage and diversity of Fagus crenata plantations established in Shizuoka Prefecture were surveyed by analyzing chloroplast DNA and nuclear microsatellites (nSSRs). Chloroplast DNA haplotypes, which are naturally distributed along the Sea of Japan side but not within the prefecture, were found in three out of the eight surveyed plantations. Two of the three plantations were also classified as the same lineage as the Sea of Japan by a STRUCTURE analysis of nSSR genotypes. Therefore, the two genetic markers used in this study revealed that the two plantations belonged to a different genetic lineage from that of the natural populations found within the prefecture (i.e. the lineage found on the Pacific Ocean side). It was concluded that these two plantations would not be suitable for the purpose of vegetation restoration from a genetic point of view. Furthermore, because of the estimated genetic diversity of the plantations using the nSSR loci, the values of allelic richness for all three plantations were lower than the average value of the natural populations in the prefecture. Therefore, we suggest that more genetically diverse seeds and seedlings are necessary to ensure more genetically diverse plantations.