Problem statement: To investigate coagulase gene variants through Restriction Fragment Length Polymorphism (RFLP) amongst clinical isolates of Methicillin-Resistant Staphylococcus Aureus (MRSA) collected from Chennai based hospitals. Approach: A total of 85 MRSA clinical isolates collected from various clinical sources were studied for the molecular typing purpose. To perform coagulase gene typing, the repeated units encoding hypervariable regions of the Staphylococcus aureus coagulase gene were amplified by the PCR followed by AluI and HaeIII restriction enzyme digestion of the PCR product and analyzed for RFLP. Results: Cluster analysis performed with Un-weighted Pair Grouping Using Arithmetic Mean Analysis (UPGMA) at >80% similarity level classified all strains into 31 and 21 genotypes based upon AluI and HaeIII RFLP patterns respectively. AluI RFLP patterns gave a high discriminatory index and proved to be better than that of HaeIII in typing of MRSA strains. Conclusion: Method investigated in this study, proved to be quick, reliable and useful for typing large number of MRSA strains from various clinical isolates with high fidelity. Grouping of strains based on RFLP patterns of both enzymes, improved the discriminatory index. Finally, using this methodology group of epidemiological strains can be typed reliably and effectively using both enzymes. Significance and impact of the study: This efficient and reliable typing procedure is beneficial to develop efficient infection control measures in hospitals for staphylococcal infection. This typing procedure could be used to analyze large number of strains with in a short period of time and thus useful for epidemiological investigations. © 2009 Science Publications.