Abstract: The inter-simple sequence repeat (ISSR) and fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) markers were used to evaluate the genetic diversity of 20 Lentinula edodes strains. Ninety-eight bands were detected by 8 ISSR primers, of which 90.82% were polymorphic. The coefficient of pairwise genetic similarity ranged from 0.520 4 to 0.989 7.A total of 13 487 CCGG sites were detected using 15 selected primer pairs. Among the sites, 1 704 were of hemi-methylation with an average rate of 12.63%, and 1 865 of full-methylation with an average rate of 13.83%. The MSAP data were further divided into methylation sensitive polymorphisms (MSP) and methylation insensitive polymorphisms (MISP) groups. A significant correlation between ISSR and MISP was found by the Mantel test, while none between ISSR and MSP. It appeared that there was a significant methylation diversity among various L. edodes which could be of value for the breeding purpose.