To explore the genetic diversity and relationships among the populations of genus Cotoneaster in the Western Tianshan Mountains of Xinjiang municipality， China， we analyzed the genetic diversity of 112 Cotoneaster plants from 15 wild populations using ISSR molecular markers. A total of 166 bands were amplified using 15 ISSR primers， of which 143 were polymorphic， yielding an average polymorphic ratio of 86.29%. The Nei′s gene diversity index （H） and Shannon′s information index （I） 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. These results indicated significant genetic differentiation among the wild populations of Cotoneaster， with a certain degree of gene exchange occurring between populations. Overall， Cotoneaster populations in the Western Tianshan Mountains of Xinjiang exhibited clear genetic differences and high levels of genetic diversity. At the population level， the Beishan Maoliugou population in Tekes County represented the highest genetic diversity. Clustering results revealed that most populations could be clustered according to their geographical locations， although some geographically close populations did not clustered together. These fingdings can provide an important reference for the effective protection and development and utilization of Cotoneaster germplasm resources in the Western Tianshan Mountains of Xinjiang municipality， China.