Isolates from Lentinus edodes cultivated bags were studied,taken Lentinus edodes 931-9 as a control.And phylogenetic analysis based on ITS and β-tubulin sequences was employed in identification of this isolate.Results showed that there was two genetically different strains in Lentinus edodes cultivated bags which were different from Lentinus edodes 931-9.This proved that the isolates of Lentinus edodes cultivated bags were different from Lentinus edodes 931-9.