Differentiation of closely related methicillin resistant staphylococcus aureus (MRSA) isolated from food chain is required for epidemiological and food safety studies. This study provided evidence for using coagulase (coa) gene sequence repeats as a powerful diagnostic tool for differentiation of closely MRSA isolated from different sources. Staphylococcal species were isolated from milk, meat, and meat-products. Staphylococcus aureus strains with identical antibiograms were differentiated using enterotoxin genotyping, coa gene polymorphism, the patterns of polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) of coa and nucleotides sequencing of coa gene-PCR products. Nine CoPs and MRSA strains were closely related and could not be differentiated by antibiogram. Six strains of them were differentiated by enterotoxin genotyping and PCR-RFLP of coa gene and three strains were accurately differentiated by nucleotides sequencing of coa gene-PCR products. In conclusion, the above findings highlight the promising role of coa repeat region nucleotide sequences in differentiation of closely related MRSA in food chain that can help in their diagnosis and epidemiological studies.