Staphylococcus aureus is well known as a major pathogen, causing a variety of nosocomial and hospital-acquired infections. Rapid and reliable detection of methicillin-resistant S. aureus (MRSA) is important for initiation of appropriate antibiotic therapy and prevention of the spread of the organism. For rapid identification of methicillin-resistant Staphylococcus aureus, molecular methods are generally targeting mecA and species specific genes. Sa442 DNA fragment is a popular species-specific target. However, recently, there have been few reports on S. aureus isolates that are negative for Sa442 fragment; therefore, use of single gene or DNA-fragment–specific polymerase chain reaction (PCR) for identification of microbial isolate may result in misidentification. As a consequence, the use of one gene as single marker may lead to misidentification, while incorporation of an additional species-specific marker could increase strain coverage and assay robustness. Therefore, the present study was aimed at the development of a species-specific PCR assay for rapid identification of Staphylococcus aureus isolates, using both nuc and Sa442 as target genes. Therefore, the present study was aimed at the development of a species-specific PCR assay for rapid identification of Staphylococcus aureus isolates, using both nuc and Sa442 as target genes.