resistant Staphylococcal aureus (MRSA) is one of the most important strains responsible for both Hospital and Community acquired infections (HA-MRSA and CA-MRSA). Spread by contact directly or indirectly. Objective: To differentiate the Isolated MRSA into HA-MRSA and CA-MRSA and Molecular characterisation of Methicillin-resistant Staphylococcus aureus isolates from the clinical specimens . Methods: A total of 348 MRSA isolates obtained from various clinical specimens and submitted to the Department of Microbiology of Regional Institute of Medical Sciences (RIMS), Imphal, during the period from October 2019 to November 2022, were studied. All isolates were confirmed as MRSA by using standard techniques [16]. PCR for detection of mec A and pvl genes was done and Antimicrobial Susceptibility testing of MRSA isolates was done by Kirby-Bauer disc diffusion method [24]. Results: All the 348 MRSA isolates, 124(35.63%) met the definition of HA-MRSA and 224 (64.36%) CA-MRSA. SCCmec typing was done in both community-acquired infection and healthcare-associated infection and mec types 4a, 66 (19.0%), III+V, 65 (18.7%), and 4a+V 63 (18.1%) were more frequently isolated. AST pattern showed that 84.57 percent (181/214) and 79.10 percent (106/134) were multidrug resistant (MDR)-CA-MRSA and MDR-HA-MRSA, respectively. Conclusion:The emerging MDR resistance pattern of CA-MRSA (84.57%) has to be controlled with proper antibiotic stewardship. This emphasizes that the diagnosis of CA-MRSA should be done appropriately by standard diagnostic tools such as molecular characterization by PCR and antibiotic-susceptibility profile to avoid treatment failures and also proper infection prevention control measure especially contact precaution measure should be follow to prevent spread of MRSA in hospital as well as in community