Dermatophytes are keratinophilic fungi that cause skin infections in both humans and animals. Recently, the incidence rates of fungal infections associated with Trichophyton spp. have been considered endemic in many locations. The aim of this study was to isolate and characterize Trichophyton spp. from canines and felines. In the present study, screened 442 canine (n = 386) and feline (n = 56) samples for dermatophytes. Among all the samples, ten isolates were identified as Trichophyton spp. based on micro-morphological features. For comparative analysis, we included three human strains of Trichophyton mentagrophytes complex. In vitro susceptibility of antifungal drugs indicated the highest sensitivity except for fluconazole. The canine and human strains were genetically characterized by sequencing three genes: the internal transcribed spacer region of rDNA, translation elongation factor 1- gene, and beta-tubulin. Based on sequence homology and phylogenetic analysis, the ten canine strains belonged to four different species/ genotypes such as T. mentagrophytes genotype VIII (T. indotineae) (n = 5), T. interdigitale (n = 2), T. simii (n = 2) and T. quinckeanum (n = 1). The three human strains used for comparative analysis were identified as T. mentagrophytes genotype VIII (n = 2) and T. benhamiae (n = 1). The study hence indicates that the T. mentagrophytes genotype VIII, considered as an endemic and emerging human pathogenic clone in India, is also the prevalent in animals.