In this study， a total of 222 samples from nine populations of ancient Liquidambar formosana Hance that distributed in Jiangxi province， P.R. China， were genotyped by capillary electrophoresis using 14 pairs of SSR primers， followed by the genetic diversity and cluster analysis using GenAIEx， CERVUS and Structure. The results showed that the average number of observed alleles （Na） of 14 SSR loci was 8.143， with the average number of effective alleles （Ne） of 2.819. The average value of Shannon information index （I） was 1.009， with a mean polymorphism information content （PIC） of 0.513. The average expected heterozygosity （He） and observed heterozygosity （Ho） were 0.504 and 0.470， respectively. The Ningdu （ND） population had the highest genetic diversity （He=0.551）， and the Wanli （WL） population had the lowest genetic diversity （He=0.394）. The South region of Jiangxi province showed the highest genetic diversity （He=0.534） and eight private alleles， followed by the North region of Jiangxi province with He=0.505 and the largest number of 14 private alleles. The lowest genetic diversity and a small number of private alleles were found in the Central region of Jiangxi province （He=0.473， n=2）. The results of AMOVA showed that the intra-population variation （92%） was significantly higher than that of the populations （8%）. This was in line with a coefficient of genetic differentiation （Fst=0.133）， implying higher gene flow （Nm=2.995）. According to principal component analysis （PCoA） and structure analysis， 9 populations could be divided into three groups， and there were different degrees of introgression among populations. Collectively， this study provided insights for the utilization and protection of ancient L. formosana， indicating the importance on the protection of ancient trees vailable in the future breeding program. In order to maximize a long-term genetic gain， the selection of superior trees in the populations in the North and South of Jiangxi province should be strengthened which may contain specific gene type resources.