Abstract: The objective of this study was to provide molecular basis for the selection of breeding material of Ganoderma lucidum content in studying polymorphism of G.lucidum monokaryon strains.The genetic diversity of 34 monokaryons of G.lucidum were analyzed by ISSR, SRAP, and RAPD markers.The results showed that a total of347 fragments were amplified, among them 308 ( accounting for 88.76% of the total) were polymorphic.The ISSRPCR had a better superiority because of the highest number and rate of polymorphism.The maximum difference of dissimilarity coefficient between 119- 123 and the rest seemingly suggested that it had mutated. UPDMA dendrogram based on ISSR, SRAP and RAPD markers indicated that the rest 33 strains could be distinguished into2 groups when dissimilarity coefficient was 0.67.Based on results of comprehensive analysis, the group II included strain 119- 180, 119- 210, 119- 212, G0119 and 119- 214, and group I included the other 28 strains. It could be concluded that polymorphism of G.lucidum monokaryon strains by ISSR, SRAP and RAPD analysis were viable, it could provide reference for mating type identification and the screening of breeding material, reducing the workload and the risk of breeding.