[Objective]This study aimed to analyze genetic differences among Flammulina velutipes monokaryon strains.[Method]Twenty F1monokaryon strains(W1-W20)of F.velutipes were separated with conventional dilution method.Fifteen SCoT primers and nine ISSR primers were screened.According to amplification results,genetic similarity coefficients among various strains were calculated using NTsys 2.10e analysis software for cluster analysis.[Result]Six primers could be use to amplify clear polymorphic bands.To be specific,a total of 327 clear DNA fragments were amplified,including 287 polymorphic bands,accounting for 87.77%of the total number of bands amplified.Based on SCoT analysis,the genetic identity(GI)among 20 strains ranged from 0.187 5 to 0.937 5;to be specific,GI between W2 and W3 and that between W11 and W12 reached the maximum of 0.9375;GI between W15 and W18 was the minimum of 0.187 5.Based on ISSR analysis,GI among 20 strains ranged from 0.250 0 to 1.000 0;to be specific,GI between W3,W4 and W9,GI between W15 and W17,and that between W16 and W19 reached the maximum of 1.000;GI between W14 and W18 was the minimum of 0.250 0.Such low genetic identity fully demonstrated great genetic differences among F.velutipes monokaryons.According to results of cluster analysis,at a similarity level of 0.55,20 F.velutipes monokaryons were significantly divided into three groups using SCoT markers;at a similarity level of 0.66,20 F.velutipes monokaryons were divided into three groups using ISSR markers.Specifically,W11,W18 and W20 were invariably divided into one group;W15 and W17 were divided into one subgroup.[Conclusion]In this study,two type of markers were used for analysis of genetic diversity among F.velutipes monokaryon strains,which provided scientific and practical basis for screening high-quality monokaryon parents of F.velutipes. [Method] This study aimed to analyze genetic differences among Flammulina velutipes monokaryon strains. [Method] Twenty F1monokaryon strains (W1-W20) of F. velutipes were separated with conventional dilution method. Fish 16 primers and nine ISSR primers were screened. According to amplification results, genetic similarity coefficients among various strains were calculated using NTsys 2.10e analysis software for cluster analysis. [Result] Six primers could be used to amplify clear polymorphic bands. To be specific, a total of 327 clear DNA fragments were amplified, including 287 polymorphic bands, accounting for 87.77% of the total number of bands amplified. Based on SCoT analysis, the genetic identity (GI) among 20 strains ranged from 0.187 5 to 0.937 5; to be specific, GI between W2 and W3 and that between W11 and W12 reached the maximum of 0.9375; GI between W15 and W18 was the minimum of 0.187 5. Based on ISSR analysis, GI among 20 ranges ranged from 0.250 0 to 1.000 0; to be specific, GI between W3, W 4 and W9, GI between W15 and W17, and that between W16 and W19 reached the maximum of 1.000; GI between W14 and W18 was the minimum of 0.250 0.Such low genetic identity fully demonstrated great genetic differences among F.velutipes monokaryons .According to results of cluster analysis, at a similarity level of 0.55,20 F. velutipes monokaryons were significantly divided into three groups using SCoT markers; at a similarity level of 0.66,20 F. velutipes monokaryons were divided into three groups using ISSR markers. Specifically , W11, W18 and W20 were invariably divided into one group; W15 and W17 were divided into one subgroup. [Conclusion] In this study, two type of markers were used for analysis of genetic diversity among F. velutipes monokaryon strains, which provided scientific and practical basis for screening high-quality monokaryon parents of F. velutipes.