Enzyme assay was carried out against wild, cultivate commercial stocks of strain and their variation stocks for analyzing their genetic differences and relations with the expression character. (1) Discrimination of various stocks of strain Flammulina velutipes : Zymograms of Esterase from F. velutipes showed many bands on the gel and variations among the different strains, and this method was very effective to distinguish the strains. The strains of F. velutipes in this experiment was largely classified to three groups (tentatively named A, B and C) according to the cluster analysis of esterase zymograms. All cultivate commercial strains belong to A group. The differ ences of physiological and morphological characteristic among the each groups were observed with mycelial growth, cap color and the size of basidiospore, and in addition these groups were different biological species each other from the crossbreeding test. (2) Screening of undesirable change in budding: The activity of peroxidase from F. velutipes was measured against normal stocks and variation stocks of strain for screening undesirable changes in budding. Also zymograms analysis of peroxidase was carried out concurrently. A specific band which is related with the germination abilities was observed on zymograms. Furthermore, a strong correlation (γ= 0.8590) between the peroxidase activities and the degree of germination abilities was found by statistical consideration. From this results it is suggested that peroxidase is one of the key enzyme in the process of germination of F. velutipes.