Vaccines against trichophytosis introduced over 60 years ago contributed to a significant reduction in the prevalence of dermatophyte infections on cattle farms. Currently, vaccination is not obligatory but commonly used and recommended by veterinarians, which is associated with the renaissance of dermatophyte infections in farm animals. Importantly, vaccine administration may cause clinical lesions imitating a virulent form of dermatophytosis. Correct determination of a possible correlation of superficial changes with the vaccine strain plays a key role in taking therapeutic measures. In this study, the usefulness of genotyping methods (melting-point-PCR and amplified fragment length polymorphism) in identification of the source of dermatophyte infection in cases correlated with vaccine administration is examined. The results revealed that dermatophytes isolated from skin lesions in calves temporarily associated with vaccine administration had an identical electrophoretic profile with the vaccine strain and differed from the reference strain of Trichophyton verrucosum CBS365.53. In conclusion, genotyping methods are a useful tool for rapid and reliable identification of the vaccine source of superficial lesions in calves. Their high resolution, speed of execution and low costs are undoubted advantages in the implementation for routine use in similar cases of dermatophyte infections.