The increase in the frequency of methicillin-resistant Staphylococcus aureus (MRSA) demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. The objective of this study is to establish variations of randomly amplified polymorphic DNA (RAPD) patterns in S. aureus isolates which are collected from clinical isolates and a systematic relationship between them. Identification of isolates and antimicrobial susceptibility tests were performed by automated system and conventional phe- notypic methods. A total of 30 out of 47 isolates (64%) expressed methicillin-resistance. When methicillin-sus- ceptible and resistance isolates were compared, the least active agents were rifampin, all aminoglycosides and penicillines, tetracycline and amoxicillin-clavulonic acid for methicillin-resistance isolates. RAPD-PCR method with 25 different primers was analyzed on 47 clinical isolates of S.aureus. All the data were employed to cons- truct dendograms using the unweighted pair group method using arithmetic (UPGMA). In this study, it is clear that, RAPD-PCR assayed with combination of five primers can be successfully applied to assess the genetic relationship between MRSA and MSSA isolates from clinical samples.