Introduction Methicillin-resistant Staphylococcus aureus (MRSA) is associated with high morbidity and mortality due to the development of antimicrobial resistance secondary to irrational use of antibiotics, nonadherence to infection control practices, and increased use of intravascular devices in healthcare systems. Detection of MRSA is critical in clinical microbiology laboratories as it helps identify MRSA carriers and avoid treatment failure in patients. Hence, this study compared various phenotypic methods with the standard genotyping method to determine a method that permits rapid and accurate detection of MRSA. Materials & Methods Staphylococcus aureus ( S. aureus ) was initially identified based on colony morphology, Gram staining, standard biochemical tests, and antibiotic susceptibility using disk diffusion. MRSA was identified based on the detection of the mecA gene by polymerase chain reaction (PCR) and subsequent gel electrophoresis. Disk diffusion using cefoxitin or oxacillin and mannitol salt agar with 6-µg/ml oxacillin were used for phenotypic detection of MRSA. The D test was used to detect inducible clindamycin resistance in S. aureus isolates. Results Of the 100 S. aureus isolates analyzed, 37% were identified as MRSA by PCR and the cefoxitin disk diffusion method; however, only 31% were detected by the oxacillin disk diffusion method and 29% by the mannitol salt agar method. The sensitivity of the cefoxitin disk diffusion test, oxacillin disk diffusion, and mannitol salt agar methods was 86.05%, 83.78%, and 70.73%, respectively. Specificity was 100% for all the three phenotypic methods (p < 0.001). Notably, inducible clindamycin resistance was found in 37.2% of the MRSA isolates, indicating potential challenges in treatment. Conclusion Among the three phenotypic methods tested, the cefoxitin disk diffusion method had 100% sensitivity and specificity, which is similar to that of PCR-based MRSA detection. Hence, the cefoxitin disk diffusion method is recommended for use in clinical laboratories, where molecular methods are not available as it is both cost-effective and easy to perform.