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Periodical surveillance on nosocomial pathogens is important for antimicrobial stewardship and infection control. The first methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) molecular surveillance in Hospital Canselor Tuanku Muhriz (HCTM), a Malaysian teaching hospital, was performed in 2009. The dominant clone was identified as an MRSA carrying SCC<i>mec</i> type III-SCC<i>mercury</i> with <i>ccrC</i> and <i>sea</i>+<i>cna</i> toxin genes. In this study, we report the findings of the second HCTM MRSA surveillance carried out in 2017, after an interval of 8 years. Antibiotic susceptibility testing, SCC<i>mec</i>, toxin gene, and <i>spa</i> typing were performed for 222 MRSA strains isolated in 2017. Most strains were resistant to ciprofloxacin, erythromycin, clindamycin, cefoxitin, and penicillin (<i>n</i> = 126, 56.8%), belong to SCC<i>mec</i> type IV (<i>n</i> = 205, 92.3%), <i>spa</i> type t032 (<i>n</i> = 160, 72.1%) and harboured <i>seg</i>+<i>sei</i> toxin genes (<i>n</i> = 172, 77.5%). There was significant association between resistance of the aforementioned antibiotics with SCC<i>mec</i> type IV (<i>p</i> < 0.05), t032 (<i>p</i> < 0.001), and <i>seg</i>+<i>sei</i> carriage (<i>p</i> < 0.05). Results from this second MRSA surveillance revealed the occurrence of clonal replacement in HCTM during an interval of not more than 8 years. Investigation of the corresponding phenotype changes in this new dominant MRSA clone is currently on-going.