Trichophyton quinckeanum, known as the causative agent of mouse favus, has been a subject of controversy since its discovery, 125 years ago. The purpose of this study was to examine the phylogenetic relationships between this fungus and related taxa. To achieve this objective, the ITS rDNA region, as well as actin and β-tubulin gene regions of various isolates were sequenced. Bayesian inference and maximum likelihood analyses were conducted with T. rubrum as outgroup. Our study showed that strains identified as T. quinckeanum and others identified as T. schoenleinii are part of the complex T. mentagrophytes, and that their genotype cannot be confused with any other dermatophytes. Furthermore, this study demonstrates that the choice of the neotype of T. mentagrophytes was inappropriate. The beta-tubulin topology also revealed that isolates of T. interdigitale form a genetically distinct population from the type strains of Arthroderma vanbreuseghemii. Therefore, contrary to what is generally accepted, the anthropophilic species T. interdigitale cannot be considered as the anamorph associated with the latter.