Methicillin-resistant Staphylococcus aureus (MRSA) has been emerged with significant morbidity and mortality in the worldwide. A variety of methods have been implemented to optimize MRSA detection, but yet, the optimal approach remains controversial. In the current review, we summarize both phenotypic and genotypic laboratory methods for detection of MRSA isolates. In summary, phenotypic methods are time-consuming and labor-intensive and suffer from inadequate sensitivity and specificity. Moreover, these methods are clearly affected by test conditions. Genotypic methods are advantageous for high sensitivity, specificity and remarkably reduced turnaround time. However, although different PCR-based methods, including Hyplex Staphyloresist PCR, GenomEra MRSA/SA, GenoType MRSA Direct, Genoquick MRSA, MD GeneOhm MRSA, BD Max MRSA, BD GeneOhm MRSA Achromopepticase, Auto-MRSA, Cepheid Xpert, LightCycler MRSA Advanced, have been utilized for MRSA detection, limitations related to false-positive results have been reported. In addition, PCR methods are associated with greater expenses. So, if laboratories are not able to afford molecular methods for routine use, simultaneous application of two phenotypic methods, one with high sensitivity and the other with high specificity, is a useful alternative. Also, it is more reasonable to choose MRSA screening method with regard to prevalence and local epidemiology of MRSA strain.