Abstract: Phellodendron amurense is a rare and endangered medicinal plant in China. We assessed the genetic diversity within and among populations of this species using AFLP. A total of 129 individuals from 10 wild populations were detected by eight pairs of AFLP primers. These primers generated a total of 1,704 bands, of which 1,581 were polymorphic. The results revealed a high level of genetic diversity. At species level, the percentage of polymorphic loci (PPL) was 92.77%, the effective number of alleles per locus (N_e) was 1.4636, Nei’s gene diversity (H) was 0.2316, and Shannon’s information index (I) was 0.4275, respectively. At population level, the estimates of PPL =54.20%, N_e=1.2487, H=0.1524 and I=0.2371. The coefficient of genetic differentiation (G_st) was 0.3420. UPGMA cluster analysis showed that there was a possible correlation between genetic variance and habitat differences. As a conclusion, we propose that conservation of P. amurense should be in their natural habitats, including Mts. Changbaishan, Wandashan, Daxing’anling, and Xiaoxing’anling, Qianshan and Yanshan. At the same time, the preservation of germplasm resources in botanical gardens should be carried out by sampling more individuals from multiple sites.