The present study was carried out to investigate usefulness and effectiveness of randomly amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) and repetitive element sequence-based polymerase chain reaction (REP-PCR) in differentiating of staphylococcal strains and to compare the results of these methods with those obtained by antibiotyping. Staphylococcal strains, obtained from various clinical samples and collected from different wards, were characterized phenotypically by susceptibility testing and genotypically by using RAPD-PCR and REP-PCR methods. It was found that there was no significant association between genotypes obtained from RAPD and REP-PCR. Strains with a similarity coefficient of 80% and 70% or greater were grouped in a cluster for RAPD-PCR and REP-PCR, respectively. RAPD-PCR was found to be very efficient with the discriminatory index (DI) of 0.91 whereas discrimination index (DI) of REP analysis was found to be 0.88 with RW3A primer and combination of REP1R-I, REP2-I primers. The findings of this study indicate that RAPD-PCR reliably distinguish ward and source-related clustering. The RAPD primers provide to discriminate MRSA, MSSA and CNS strains whereas REP analysis could not be as discriminative as RAPD. Therefore, RAPD-PCR, evidenced to be inconsiderably more discriminatory than REP-PCR, is well suited for fast and accurate strain identification.