Multilocus microsatellite typing (MLMT) was performed on 93 strains of Microsporum canis (M. canis) isolated between 2012 and 2017 from 75 cats, 8 dogs, and 10 pet owners. These strains were derived from 2 major reservoirs: commercial breeding facilities and pet shops (PS), and stray cats and pet cats that went outdoors and came in contact with stray cats (Outdoor). Six microsatellite markers were used for genotyping. These 93 strains included 22 genotypes; 11 had been previously detected in Japan while the other 11 were new. Strains belonging to the previously reported genotypes, P and A, were distributed widely throughout Japan. Genotype P was the most frequent, accounting for 37 (39.8%) of the 93 strains. Most were derived from Outdoor sources. Genotype A was the second most frequent (11 of 93 strains, 11.8%). Most of the genotype A strains were derived from the PS reservoir. All new genotypes were detected in isolates from cats. Many of these were derived from the Outdoor reservoir. Consistency of infection was observed in 18 of the 19 familial cases. These findings indicate that genotypes differ in strains derived from PS and Outdoor reservoirs. MLMT genotyping is useful for tracking the routes of spread and transmission of M. canis in Japan.