Abstract: 48 Ganoderma lucidum germplasm resources from different geographical regions were used as samples, and the genetic diversity of Ganoderma lucidum was studied by using ITS and ISSR molecular markers, in order to better display the genetic diversity of different Ganoderma lucidum strains by using genetic information data.The results showed that 48 strains of Ganoderma were divided into Ganoderma lucidum（35）,Ganoderma resinaceum（11）,Ganoderma sichuanense（1） and Trametes cubensis（1） by ITS sequence amplification and sequencing.A total of 53 bands were amplified by 5 ISSR primers, the percentage of polymorphic bands was 96.23%,the Nei′s gene diversity was 0.27,the Shannon′s information index was 0.43.The genetic similarity coefficient of ISSR marker was about 0.70,and 48 strains of Ganoderma were divided into three groups.The first group was 11 strains of Ganoderma lucidum,the second group was 29 ‘Penjing 1’,and the remaining strains were the third group, indicated that the combination of two markers could explain the genetic relationship between different strains in more detail.Strains 16 and 17 were both Ganoderma lucidum,and the genetic similarity coefficient of ISSR molecular markers reached 0.98,suggested that they might be the same variety, which was a synonym phenomenon in production.The ISSR primers selected for PCR amplification in this study had good polymorphism and high stability, which could effectively distinguish sessile Ganoderma lucidum from other Ganoderma lucidum,and reveal the genetic diversity and population genetic structure of the germplasm, which could provide reference basis for the protection of Ganoderma lucidum germplasm resources and the selection of high-quality germplasm materials, so as to better promote the healthy development of Ganoderma lucidum industry.