In order to select suitable Hevea accessions for extending genetic base of Chinese rubber tree in future breeding schemes, the genetic diversity of 14 wild accessions and 25 cultivated clones were detected by RAPD and ISSR. 31 reliable primers (19 RAPD primers and 12 ISSR primers) were chosen. A total of 232 bands were generated with the informative primers. The cultivated clones showed less polymorphism than the wild accessions, the coefficient ranged from 0.584 to 0.880, and it ranged from 0.639 to 0.931 in cultivated clones. The 39 accessions were divided into 3 clusters on the basis of unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis. Cluster I contained nine wild accessions. Cluster II consisted of 24 cultivated clones and 5 wild accessions, and Cluster III only contained one cultivated clone, some cultivated clones, i.e. PR107, Reyan 217, could be screened from 39 accessions. All of the results can be used in future Hevea breeding programs. It is proven that RAPD and ISSR can be used in Hevea clonal identification and diversification and diversity study.