Abstract:To reveal the genetic diversity of germplasm resources of Canarium album in China, the genetic diversity of 86 germplasms selected from the major distribution areas was studied by using ISSR and RAPD markers, and core germplasms were constructed. The results showed that 86 germplasms could be divided into 3 groups based on UPGMA genetic similarity, and 4 groups by using STRUCTURE cluster analysis, which basically conform to the regional distribution of C. album in China. The overall genetic diversity coefficient using ISSR and RAPD was 0.284±0.169 and 0.244±0.163, the percentage of polymorphism loci was 92.56% and 100%, the genetic differentiation coefficient was 0.127 and 0.142, the gene flow was 3.423 and 3.025, the average genetic similarity coefficient between populations was 0.930 and 0.939, and the average genetic similarity coefficient between individuals was 0.736 and 0.732. Therefore, it was suggested that the rich genetic diversity of C. album in China mainly caused by the genetic differentiation or variation among individuals, and there were obvious regional differences.