Abstract:The genetic diversity of Aquilaria sinensis (Lour.) Gilg was investigated by using ISSR molecular markers. The results showed that there was high genetic diversity at the species level, and relatively low at the population level, in which the Maoming population (MM) had the highest genetic diversity. Significant genetic differentiation was found among populations of A. sinensis with GST＝0.4425, it showed that the genetic differentiation within population was bigger than that between populations. The analyses of UPGMA and PCA revealed that 8 populations of A. sinensis were divided into two lineages, lineage Ⅰincluded 5 populations located in Guangdong (MM, GG and GZ), Fujian (FJ) and Hainan (HN), and lineage Ⅱ comprised 3 populations in Guangxi (GX) and Yunnan (YX and YM). At species level, the gene flow with Nm＝0.6633<1 was very limited, which lead to high differentiation among populations. The limitation of gene flow mostly occurred between two lineages, while the gene flow was frequent within lineage with Nm>1 in recent historical period. The main reason of genetic differentiation was geographical factors, which Yunkai Mountains located at borderline of two lineages hindered the gene flow between two lineages.