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Intro: Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of hospital-acquired infections (HAI) worldwide. SCCmec elements and an arsenal of virulence factors in their genome contribute to the emergence of antibiotic resistance and highly pathogenic S. aureus that eventually result in significant morbidity and mortality. This study aims to describe genes that are potentially associated with HAI-MRSA occurring in a local major tertiary hospital. Methods: A cross-sectional study was conducted from May 2020 to June 2022. The bacterial strains isolated from various clinical samples were collected from a main tertiary hospital in Kuala Lumpur. These isolates were confirmed as MRSA by MALDI-TOF, coagulase test and antibiotic susceptibility tests. All isolates were screened for virulence genes and typed for SCCmec using multiplex PCR. Findings: A total of 240 clinical MRSA isolates were screened in this study. Majority of the isolates were from blood specimens of patients admitted to the medical department. The prominent virulence genes identified were hlα followed by hlβ. Most of the isolates harboured SCCmec type IV and conferred resistance against cefoxitin (100%), erythromycin (70%), and clindamycin (64%). Discussion: SCCmec type III was previously shown to be the most prominent type globally for HAI. However, epidemiological change of SCCmec type was observed in this study where SCCmec type IV was the most prevalent in our study site. Conclusion: Local surveillance of SCCmec types and virulence genes is pivotal for better characterisation and control of MRSA-associated HAI.