The genetic diversity of seven populations of Quercus variabilis, which grows in secondly forests, was analyzed using 10 nuclear simple sequence repeat（SSR）markers and 6 chloroplast（cp）SSR markers. Only one cpDNAhaplotype was detected from all individuals suggesting historical bottleneck and resent rapid expansion. Nuclear genetic diversity was high（average RS=4.58、HE=0.694）and the populations were differentiated moderately（F’ST＝0.087-0.100）. The STRUCTURE analysis detected two clusters, and all populations, except for northenmost population, showed admixure of these two clusters. The phylogeographic structure, which many Japanese natural trees exhibited, was not observed in Q. variabilis. These results did not conflict to human impacts on the genetic structure of Q. variabilis. The influence of hybridization with closely related species, Quercus acutissima, was evaluated. All individuals of Q. acutissima had the same single cpDNA haplotype as Q. variabilis. Nuclear DNA analysis showed clearly differentiation between two species, but genetic admixturewasobservedin twopopulationswhichtheygrewsympatrically. Theseresults suggest that not only historical distribution changes but also impacts of human activity and hybridization with Q. acutissima have to be considered to comprehend the genetic structure of Q. variabilis.