Taxonomic delineation of etiologic agents responsible for recalcitrant dermatophytosis causing an epidemic in India is still debated. The organism responsible for this epidemic is designated asT. indotineae, a clonal offshoot ofT. mentagrophytes. To evaluate the real identity of the agent causing this epidemic, we performed a multigene sequence analysis ofTrichophytonspecies isolated from human and animal origin. We includedTrichophytonspecies isolated from 213 human and six animal hosts. Internal transcribed spacer (ITS) (n= 219), translational elongation factors (TEF 1-α) (n= 40), ß-tubulin (BT) (n= 40), large ribosomal subunit (LSU) (n= 34), calmodulin (CAL) (n= 29), high mobility group (HMG) transcription factor gene (n= 17) and α-box gene (n= 17) were sequenced. Our sequences were compared withTrichophyton mentagrophytesspecies complex sequences in the NCBI database. Except for one isolate (ITS genotype III) from animal origin, all the tested genes grouped our isolates and belonged to the “Indian ITS genotype”, currently labeled asT. indotineae. ITS andTEF 1-αwere more congruent compared to other genes. In this study, for the first time, we isolated theT mentagrophytesITS Type VIII from animal origin, suggesting the role of zoonotic transmission in the ongoing epidemic. Isolation ofT. mentagrophytestype III only from animal indicates its niche among animals. Outdated/inaccurate naming for these dermatophytes in the public database has created confusion in using appropriate species designation.