Microsporum canis is a zoophilic dermatophyte, which is very contagious, especially to cats and dogs. Asymptomatic animal carriers of M. canis are regarded a critical factor in the epidemiology of the disease. The aim of this study was to investigate the epidemiological origin of M. canis isolates using morphological traits in combination with molecular analysis. Identification of dermatophyte strains was carried out by correlating the clinical manifestation of the infection with a micro- and macroscopic examination. To confirm the species affiliation fully, molecular differentiation methods were used. A positive result of the culture examination was obtained from the samples with arthrospores in the direct analysis, that is, from a symptomatic cat and humans, and from a cat without any signs of infection. The microsatellite-primed PCR fingerprinting (MSP-PCR) electro-profiles were identical for all analysed strains. The melting profile-PCR (MP-PCR) electrophoregram indicated variability of the genomes of the strains. The search for the source of the infection indicated one cat that did not have any signs of dermatophytosis. PCR-fingerprinting techniques are useful tools for epidemiological investigation of the origin of dermatophyte infection. These methods can also be used in many cases for species identification of dermatophytes and clarification of the relationships among varieties of a species.