In order to develop a novel method of obtaining monokaryons for a mycorrhizal fungus, Lyophyllum shimeji, monokaryotization of dikaryotic stock culture via protoplast formation and regeneration was performed using 12 dikaryotic stocks. From 6 dikaryotic stocks, a total of 120 monokaryons were isolated, and their mating compatibility was tested. Mating-compatible monokaryons were successfully derived from a dikaryotic stock (NBRC 100325), and monokaryons of only 1 mating type relative to the parental dikaryons were isolated from another 3 strains (MH01710, OK2L-1, and HY7L-1). We successfully prepared monokaryotic stocks via protoplast monokaryotization, a technique that can be used to identify biological species of L. shimeji. This technique could be used for breeding various mycorrhizal mushrooms, including Tricholoma matsutake, for which the preparation of monospore cultures is extremely difficult.