Aim Methicillin resistant Staphylococcus aureus (S. aureus) is a major human pathogen which causes a wide range of hospital and community-acquired infections worldwide. Our objective is to describe the prevalence of MRSA within Puducherry, India. Methods A total of 172 patients treated with incision and drainage of soft tissue infections from March 2009 to September 2010 were included in the present study. We examined the antibiotic sensitivity pattern and the distribution of genes among MRSA isolates. Results In total, 72 isolates were obtained of which 51 were MRSA and 21 were methicillin sensitive S. aureus (MSSA). All the isolates showed absolute resistance pattern against beta lactam antibiotics (penicillin, ampicillin, amoxicillin) and were found to be sensitive towards macrolide and lincosamide antibiotics. The gene distribution among MRSA isolates showed the presence of femA, mecA, and lukS in 100, 94.4 and 69.4 % of the isolates respectively. The antibiotic sensitivity pattern and molecular characterization showed an increased prevalence of community acquired MRSA (CA-MRSA) in the study population. Conclusion The MRSA isolates were found to be sensitive to macrolide and lincosamide antibiotics but MSSA showed resistance pattern to the same. In this regard these antibiotics can be used for the effective treatment of MRSA at the expense of MSSA among the study population.