Abstract: Objective This study aimed to conduct genetic diversity analysis of golden flower fungus from different geographical sources based on the ISSR molecular marker technology， so as to provide a scientific basis for classify， evaluate， develop， and utilize of golden flower fungus resources.Method The ISSR molecular markers were used to conduct a genetic diversity analysis of 61 strains of golden flower fungus from Yiyang in Hunan Province， Xianyang in Shaanxi Province， Hengzhou in Guangxi Province， and Wuzhou in Guangxi Province. The genetic similarity coefficients among different strains were calculated using NSYSpc 2.10e， the cluster analysis was conducted through unweighted pair-group method with arithmetic mean （UPGMA）， and the parameters related to genetic diversity were calculated using PopGene 1.32.Result A total of 168 loci were amplified using the 11 ISSR primers， among which 158 were polymorphic loci， and the polymorphism ratio was 94.0%. UPGMA cluster analysis showed that the genetic similarity coefficients among the 61 tested golden flower fungus strains ranged from 0.48 to 1.00. When the genetic similarity coefficient was 0.60， the 61 tested golden flower fungus strains were divided into five groups： GroupⅠAspergillus cristatus， Group Ⅱ Aspergillus chevalieri， Group Ⅲ Aspergillus pseudoglaucus， Group Ⅳ Aspergillus cibarius， and Group Ⅴ Aspergillus ruber. The genetic consistency degree of Nei’s among the four geographical groups ranged from 0.7409 to 0.9967， with an average value of 0.8607. The genetic distance ranged from 0.0033 to 0.3000， with an average value of 0.1560. Among them， the genetic distance between the population in Xianyang， Shaanxi Province and the population in Yiyang， Hunan Province was the smallest， and their genetic consistency of Nei’s was the highest； while the genetic distance between the Wuzhou population in Guangxi Province and the Yiyang population in Hunan Province was the largest， and their Nei’s genetic consistency was the lowest. For the 61 tested golden flower fungus strains， the average Nei’s genetic diversity index （H'） was 0.2622， the average Shannon’s information index （I） was 0.4082， the genetic differentiation coefficient among populations was 0.4228， and the gene flow value of populations was 0.6825.Conclusion The strains of golden flower fungus enjoy rich genetic diversity. The classification of ISSR groups has a certain correlation with the species classification of golden flower fungus. No obvious correlation is found between genetic diversity and geographical origin of the same fungus.