Polymerase chain reaction (PCR) fingerprinting detected DNA polymorphisms among frequently isolated species and strains of the genera Trichophyton, Microsporum and Epidermophyton. The patterns generated by this DNA-based method permitted species and strains to be identified. The conventional methods to identify dermatophytes rely on the expression of characteristic morphological features, as well as several physiological properties. Identification is often delayed or problematic because isolates may be slow to form conidia or produce atypical microscopic structures or colony appearances. Using non-specific primers such as (AC)10, (GTG)5, M13 core sequence and AP3, characteristic PCR profiles were generated for 17 species. Intraspecies variables were also observed for four of six varieties of T. mentagrophytes, whereas no detectable DNA variability was found within the three varieties of T. tonsurans. Comparing species-specific PCR fingerprints of clinical isolates with those of type strains, species could be identified by their PCR fingerprints, even if they could not be identified by the accepted phenotypic characteristics.