To determine the relationships among Trichophyton species we constructed three phylogenies, based on the nucleotide sequences of the actin, rRNA and DNA topoisomerase II genes. These phylogenies showed several conflicting branch points. For example, strains of T. verrucosum,T. concentricum and T. mentagrophytes var. erinacei were mingled with strains of Arthroderma benhamiae and could not be separated into their own phylogenic groups. In addition, strains of A. vanbreuseghemii, T. tonsurans, T. mentagrophytes var. interdigitale and T. mentagrophytes var. quinckeanum were mingled with strains of A. simii and could not be separated into their own phylogenic groups. T. rubrum and T. violaceum made up a clade, which was phylogenetically related to the A. benhamiae clade or A. simii clade, depending on the gene examined. These findings indicate the need to reevaluate the boundaries among Trichophyton species using an alternative to morphological or molecular biological methods.