Abstract: In this study, 24 germplasm samples of Carya cathayensis were collected from Qifeng town, Anlong county, Qianxinan prefecture, Guizhou province, and genetic diversity was analyzed by ISSR molecular markers and amplified by 5 selected ISSR primers. The results showed that the 5 primers amplified a total of 30 sites, including 26 polymorphic sites, and the polymorphism site ratio（PPB） was 86.67%. The number of effective alleles（Ne）, Shannon information diversity index（I） and Nei gene diversity index（He） were 1.579 8, 0.491 6 and 0.334 4, respectively. Based on UPGMA clustering analysis, the 24 germplasms could be divided into four groups while the genetic similarity coefficient was 0.712. The results showed that the genetic diversity level of C. cathayensis was relatively high, and ISSR molecular markers could be used to study the genetic diversity of C. cathayensis, which provided a reference for the identification and classification of varieties resources of C. cathayensis.