Genetic diversity and genetic differentiation of 11 Manglietia yuyuanensis provenances from main distribution area were analyzed using ISSR molecular markers.A total of 108 amplified loci were detected by 9 primers,of which the proportion of polymorphic loci was 86.11%.A high degree of genetic diversity in M.yuyuanensis was detected,and the genetic diversity index in species level was 0.282 7,which was markedly higher than that of M.decidua and M.patungensis,the rare and endangered species belonging to the same genus with M.yuyuanensis.The result showed that there was significant difference in genetic diversity among provenances.Provenances from north and north-west Fujian province and the nearby area,including Shaxian,Jian’ou,Wuyishan of Fujian and Longquan of Zhejiang,had higher genetic diversity,which were the dominant regions to be protected and utilized. Small population effect brought by habitat fragmentation and distance isolation effect resulted in high genetic differentiation among provenances,which contributed to 25.89% of total genetic variation,and the differentiation within provenances contributed to 74.11% of total genetic variation.Results also showed that the genetic distance amog provenances was not significantly related to the geographical distance amog provenances.Based on the Nei’s unbiased genetic distance,11 provenances might be obviously divided into 3 clusters.Shaxian and Jian’ou of Fujian with high genetic diversity and large nature population was clustered into one group.The genetic distance among Huangshan of Anhui,Longquan and Kaihua of Zhejiang,Wuyishan,Shaowu and Liancheng of Fujian,and Lichuan and Longnan of Jiangxi was small,then the above provenances were clustered.Quannan of Jiangxi,located at the south of distribution area,was an individual provenance.Based on the characteristic of its wider leaves,it was conferred that Quannan provenance was mistaken for M.fordiana Oliv.in the course of seed collection.