The laccase activities of 13 strains of medicinal and edible mushrooms from the Flammulina genus (F. velutipes, F. rossica, and F. fennae) were studied. The effects of both fungal isolates and culture media were investigated. The laccase activities indicated significant differences among Flammulina strains (P < 0.001), and the cultural media significantly affected the laccase activities in Flammulina spp. (P < 0.001). The morphological characteristics of the 3 Flammulina species were similar, but differences in phylogenetic analysis and laccase activity existed among different species. Although isolates of each Flammulina species differed, the laccase variables among different Flammulina species were greater than those within the same species. The presence of simple carbon and nitrogen sources increased the maximum laccase enzyme activity, but the occurrence of both laccase activity and maximum laccase enzyme activity was delayed compared with lignocellulosic material. The laccase activities of most Flammulina isolates were increased when exposed to copper ions. Our findings offer insights into laccase productivity in response to different Flammulina species or strains and different submerged fermentation treatments.