Wild populations are important germplasm resources， and studying their genetic diversity and variation pattern of local wild and cultivated populations can facilitate their scientific protection and sustainable utilization. This study is based on the natural and cultivated distribution area of Chinese chestnut in Beijing， collecting leaves from a total of 93 germplasm of 5 cultivated populations and 1 wild population， and collecting leaves from a total of 16 germplasm of 1 population （as an outgroup） in Yichang （YC）， Hubei. Sixteen pairs of microsatellite primers （SSR） were used to analyze the genetic diversity and genetic structure. The wild C. mollissima populations in Beijing was found with relatively high genetic diversity， and the genetic diversity of the wild Hongluosi population （HLS） was significantly higher than that of other populations. There was significant genetic differentiation between populations of C. mollissima （Fst = 0.232）， with low frequency of gene flow （Nm = 0.547）. AMOVA analysis showed that the intra-population genetic variation （57.70 %） was greater than that among populations （42.30%）. The genetic structure analysis showed that YC chestnut population was significantly different from Beijing chestnut populations. The HLS wild population was independent of Banliyuan population （BLY， an ancient tree population） and the other cultivated populations that were clustered into a group， indicating that cultivated chestnuts might come from the ancient tree population in Beijing. A coincidence was observed as well based on the UPGMA clustering， PCoA and PCA analysis. Treemix analysis showed that the chestnut populations in Beijing were likely from the YC population in southern China， indicating an evolutionary path for chestnut to migrate from central China to Beijing. The population history results indicate that the Beijing populations differentiated from the YC populations approximately 83，000 years ago， while the differentiation of local wild and cultivated species in Beijing occurred approximately 32，000 years ago. Our results support the hypothesis of chestnut migrating northward from central China. The domestication of cultivated species reduced the genetic diversity of chestnut germplasm resources in Beijing. The wild populations and cultivated ancient trees retain high genetic diversity， which should be protected preferentially.