Summary Objective Dermatophytes are taxonomically classified in the genera Trichophyton, Microsporum, and Epidermophyton. Pleomorphism, cultural variability, slow growth and sporulation, and the need for additional physiological tests make dermatophytes notoriously difficult to identify. The present study aimed to compare the results of morphological and molecular identification of certain groups of clinical isolates of dermatophytes with a view to evaluating the accuracy of molecular methods. Patients and methods For each sample, the ITS1-5.8S-ITS2 rDNA region was amplified using the primers ITS1 and ITS4. PCR products were subjected to restriction fragment length polymorphism (RFLP) analysis using the enzyme MvaI and isolate identification was performed by comparing the electrophoretic RFLP patterns with reference profiles obtained previously. Finally, paired comparative analyses of molecular and conventional methods were performed. Results While morphology results from routine daily reports of the laboratories indicated that 18 (6.8%) and 136 (52.10%) of the isolates were T. rubrum and T. interdigitale, respectively, PCR-RFLP results suggested that T. rubrum was the most common etiological agent of ringworm accounting for 94 (36.01%), followed by T. interdigitale accounting for 71 (27.20%). Interestingly, 80.8% out of the 94 isolates identified as T. rubrum by molecular testing had been identified by morphological examination as belonging to different species, such as T. interdigitale (75.5%), E. floccosum (2.1%) and M. canis, T. verrucosum, and T. tonsurans (each 1.06%). Ten strains out of 261 (T. interdigitale, n = 8; E. floccosum, n = 2) had been defined as unknown species by morphological tests. Conclusion An unexpected high percent of isolates identified as T. interdigitale by conventional methods were in effect T. rubrum shown by PCR-RFLP, and regarding the necessity of correct identification of dermatophytes recovered from different clinical forms of the infection, we highly recommend ITS-sequencing or ITS-RFLP of the isolates, particularly for epidemiological research studies.