T. equinum is the main cause of dermatophytosis in horses, all over the world the identification and differentiation between T.equinum species by conventional methods has drawbacks of being very slow, often requiring weeks of culture and suffering complications of overgrowth with commensals so the molecular approaches are applied recently for diagnosis of dermatophytes. This study involved identification of T.equinum by conventional methods and application of PCR by using non-specific simple repeat sequence (GACA)4. The result showed that identification of T.equinum var. equinum and T.equinum var. autotrophicum and the primer was able to amplify both species forming characteristic PCR profiles for each.