Staphylococcus aureus is a primary cause of food poisoning and many types of other infections in humans and animals. This study aims to detect methicillin-resistant S. aureus (MRSA) in raw cow milk collected from different farms in Istanbul, using polymerase chain reaction-based phenotyping and genotyping. A total of 406 raw milk samples were collected from 6 different dairy farms located in Istanbul at different times and under appropriate conditions. The samples were transferred to laboratory under cold storage conditions. After S. aureus had been isolated from the samples by phenotypic methods, MRSA strains were detected in isolates by both phenotypic and genotypic methods. Of the 406 milk samples examined, S. aureus strains were detected in 119 (29.31%). From the 119 isolated S. aureus strains, there was merely 1 (0.84%) strain with MRSA in phenotypic and genotypic terms. Strategies required to control antimicrobial resistance should be developed and implemented in the field of veterinary and human medicine.