Introduction Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major pathogens of nosocomial infections throughout the world. In the medical field, it is extremely important to this pathogen’s trends when considering infection control.Hypothesis/Gap Statement We hypothesized that clarifying the characteristics of clinically isolated MRSA would contribute to infection control and proper use of antimicrobial agents against MRSA.AimThe purpose of this study is to elucidate the genetic and biological characteristics of the MRSA isolates found at our hospital and to reveal changes in the spread of this pathogen in the local area where we live.MethodologyPulse-field gel electrophoresis (PFGE) and polymerase chain reaction were used for the genetic analyses of MRSA isolates. Toxin production by each isolate was examined using toxin-specific detection systems.ResultsDuring the 3 years from 2017 through 2019, over 1000 MRSA strains were isolated at our hospital. Genomic analysis of 237 of these clinical isolates by PFGE revealed 12 PFGE types (types A to L), each consisting of five or more MRSA clinical strains with over 80% genetic similarity. Examination of the SCCmec genotypes found that 219 of 237 isolated MRSA strains (approximately 92%) were SCCmec genotype II or IV and that only four of the isolates carried the Panton−Valentine leukocidin (PVL) gene. Examination of the toxin production of the isolates using staphylococcal enterotoxin detection kits found that most isolates carrying the SCCmec genotype II produced enterotoxin B and/or C, and that most isolates carrying the SCCmec genotype IV produced enterotoxin A.ConclusionThe present results revealed that MRSA isolates with common properties were isolated at certain rates throughout the 3 year study period, suggesting that relatively specific MRSA clones may have settled in the local area around our hospital. We also examine the relationship between antimicrobial usage over time and changes in MRSA isolation rates.