To discuss the application of 2 kinds of molecular markers in genetic diversity of cultivated Aquilaria Lam. The genetic diversity of 17 populations of Aquilaria Lam. from Hainan, Yunnan, Guangdong, Guangxi et al was analyzed using ISSR and AFLP. 14 ISSR primers and 8 AFLP primer combinations deteted 119 and 919 loci of which the number of polymorphic loci was 88 (73.95%) and 799 (86.94%) respectively. The results of ISSR and AFLP revealed Aquilaria Lam. possessed higher genetic diversity. Because of different mechanism of ISSR and AFLP, some differences existed in the results obtained. Genetic diversity parameters based on AFLP were higher than those based on ISSR, which was probably resulted from the higher detection efficiency of AFLP. Although some differences existed between the UPGMA dendrograms of ISSR and AFLP based on the Nei’s genetic distances, Mantel test revealed obvious correlation between genetic identity matrix between ISSR and AFLP (r=0.7705, P=0.0003). Both methods could be used to analyzed the genetic diversity of Aquilaria Lam.