Background: The aim of present study was evaluation and comparison of widely used molecular techniques including pulsed-field gel electrophoresis (PFGE), multi locus sequence typing (MLST), Staphylococcus aureus protein A typing (spa), Staphylococcal Cassette Chromosome typing (SCCmec), and SCCmec typing with recently introduced method using direct repeat unit (dru) sequencing in the hyper-variable region of the SCCmec cassette for clustering and discrimination of MRSA isolates. Material and Methods: Out of 389 already molecularly established methicillin-resistant Staphylococcus aureus (MRSA) isolates 61 representative samples were subjected to PFGE and dru typing methods according to guideline. Results: The results showed that isolates were typed by PFGE typing, MLST typing, spa typing, SCCmec was typing and dru typing to 7,6,6,12,19 different types respectively. Evaluation of the discriminatory power for each method identified dru typing and PFGE as the most discriminatory methods. Conclusion: Although the discriminatory ability of dru typing, especially with closely related MRSA ST239 strains underscore its utility as a feasible and cheap method in epidemiological investigation of MRSA, we suggest the use of the conjugation of dru typing and PFGE typing for epidemiological surveillance studies, since this combination provides more discriminatory and typeability which is useful for the control of nosocomial infection.