Patterns of protein expression in the monokaryons and the derived dikaryon of the basidiomycete Flammulina velutipes were investigated using two-dimensional polyacrylamide gel electrophoresis and silver staining. Over 300 spots were detected on each gel, and 19 proteins were expressed in the dikaryon before fruiting treatment but not expressed in the monokaryon before fruiting treatment. On the other hand, 9 proteins were expressed in the monokaryon specifically. Newly expressed proteins increased after fruiting treatment (at 7 d and 14 d), but decreased after fruit bodies were formed (at 21 d). The number of newly expressed proteins after the fruiting treatment was similar in the monokaryon. Proteins expressed characteristically were classified into 7 types. The highest number of proteins (13 proteins) were specifically expressed in the dikaryon at 14 d when the fruit-bodies were formed. Twenty-seven proteins were expressed specifically in the fruit body. Fruit body specific proteins Pf1 and Pf3 were sequenced. This revealed Pf1 and Pf3 had amino acid sequences that were similar to each other, as well as a high similarity to the deduced amino acid sequence of the FDS gene isolated from F. velutipes.