In order to explore the genetic diversity and genetic relationship among the populations of Cotoneaster in the Western Tianshan Mountains of Xinjiang, the genetic diversity of 112 Cotoneaster plants from 15 wild populations in the Western Tianshan Mountains of Xinjiang was analyzed by ISSR molecular markers. A total of 166 bands were amplified by 15 ISSR primers, of which 143 were polymorphic bands, with an average polymorphic band ratio of 86.29 %. The Nei ''s gene diversity index(H) and Shannon’s information index(I) of 112 Cotoneaster species from 15 wild populations in Western Tianshan Mountains were 0.2124 and 0.3254, respectively. The genetic differentiation coefficient(Fst) among populations was 0.4259, and the gene flow(Nm) was 0.6740. It is believed that the degree of genetic differentiation at the level of wild populations of Cotoneaster is great and there is a certain degree of gene exchange among populations. The genetic differences of Cotoneaster in the western Tianshan Mountains of Xinjiang are obvious at the overall level, and the genetic diversity is high. At the population level, the genetic diversity of Beishan Maoliugou population in Tekes County was the most abundant. The clustering results showed that most of the populations could be clustered according to the geographical location, but some of the geographically close populations were not clustered together. The results of this study can provide an important reference for the effective protection and development and utilization of Cotoneaster germplasm resources in the Western Tianshan Mountains of Xinjiang.