Background: Methicillin resistant Staphylococcus aureus (MRSA) have become a global health problem causing infections in both humans and livestock, ranging from skin and soft tissue to life threatening blood stream infections. The mecA gene is known to confer resistance to MRSA isolates. This study investigated the carriage of mecA gene by MRSA isolates from pigs. Methods: One hundred non duplicate staphylococcal isolates recovered from blood samples of pigs in Bariga district of Lagos State at the Molecular Biology and Biotechnology unit of the Nigerian Institute of Medical Research were used in the study. S. aureus was identified by cultural characteristics, and positive catalase, coagulase and deoxyribonuclease tests. Phenotypic methicillin resistance was determined by the modified Kirby Bauer disk diffusion method and mecA gene was detected by conventional polymerase chain reaction (PCR) assay. Results: Twenty-five S. aureus were identified, of which 11 (44%) were MRSA by phenotypic method. All the isolates were mecA negative on PCR. Conclusion: The MRSA phenotype observed in the pig isolates in this study appears not to be the classical mecA mediated resistance. There may be alternative mechanisms of resistance in MRSA isolates in pigs.