Background: Staphylococcus aureus is a gram-positive coccus frequently found in the nose, respiratory tract, and on the skin. Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium responsible for several difficult-to-treat infections in humans. Quinolone resistance among Staphylococcus aureus emerged quickly, more prominently among the methicillin-resistant strains. Fluoroquinolones cannot be used as anti-staphylococcal agents effectively and its efficacy was dramatically reduced. Aim: The study is aimed to examine the mechanisms of fluoroquinolone resistance and to rule out the epidemiologic factors which contribute to the prevalence of antibiotic resistance in clinical settings. Methodology: Biochemical tests and antibiotic sensitivity procedure were done among the isolates obtained from various clinical samples. In our study a representative population of fifty isolates of resistant Staphylococcus aureus by both disk diffusion and agar dilution were subjected to real time PCR assay for detection of topoisomerase iv and gyrase. Result & Discussion: The incidence of MRSA in our study was found to be 74%. High prevalence of MRSA (64%) was observed from pyogenic infections followed by blood stream infections.