Phellodendron amurense Rupr. is a valuable timber species and a key species in the plant communities of Changbai Mountain in Jilin province; however, due to over-harvesting and utilization, its quantity and quality have clearly declined.. Therefore, based on its distribution on Changbai Mountain in Jilin province, 10 representative populations of P. amurense were selected, and their genetic diversity was investigated using the Inter-Simple Sequence Repeat (ISSR) technique. Using the ISSR data, the Nei and Shannon indices were determined to estimate the genetic variation of the 10 populations. This study aims to provide foundational data for preservation and protection of P. amurense. Using 60 ISSR primers to screen the 10 representative populations of P. amurense, 99 bands were amplified; 54 bands were polymorphic (54.5%). The polymorphism of the 10 populations ranged from 18.52% to 37.96%; the Hunchun population showed the greatest polymorphism, at 37.96%, the Lushuihe population showed the least, at 18.52%, and the average was 26.02%. The Shannon index ranged from 0.1103 to 0.1949, with an average of 0.1522. The Nei index ranged from 0.0759 to 0.1327, with an average of 0.1043. According to Nei's method calculation of Phellodendron amurense 10 population genetic diversity is the DST=0.1586, the differentiation index (GST=0.6183, gene flow coefficient nm is 0.3086... The total genetic variation of 61.83% of the variation existed among populations, and the variation within population was only 38.17%..A cluster map of the unweighted pair-group method with arithmetic means(UPGMA) relationships, using the ISSRs as molecular markers, was constructed. The 10 populations could be divided into two groups: 1) Songjianghe, Lushuihe, Wangou, Ji-an, and Huinan provinces, and 2) Baishi Shan, Wangqing, Antu, Yanji, and Hunchun provinces. Based on the genetic structure of P. amurense, protection measures were put forward, including guidance to create a medicinal or timber forestry. The local plant resources background investigation and summary of resources (including compartments, sub-compartments, each plant's age, height, diameter, height under crown and crown). To select the local dominant groups to carry on in situ conservation. Ex situ conservation strategies should be used to increase the number of individuals; in the Baishan area, the Songjianghe, Lushuihe provinces should be selected, in the Tonghua Area,the Ji-an provinces should be selected,in the Yanbian area, the Wangqing and Baishi Shan provinces should be selected. Artificial propagation of P. amurense should be used to promote the gradual recovery of populations, and resource manual registration should be established.