Methicillin‐resistant Staphylococcus aureus (MRSA) has been shown to be the predominant life‐threatening pathogen in Egypt. MRSA is a major cause of severe healthcare‐ associated (HA) infections. During the last decades, the incidence of community‐associated (CA) MRSA infections has a complex epidemiology arising from the circulation of different strains in the general population. Moreover, livestock‐ associated (LA) MRSA emerged recently becomes an emerging threat to public health. Therefore, it is important to illuminate the differences between CA‐, HA‐ and LA‐MRSA to shed light on their genetic diversity and evolution. This study presents the first data on analysing the correlation between CA‐, LA‐ and HA‐MRSA using antibiogram typing, molecular characteristics and antimicrobial resistance and virulence genes’ profiles. Overall, HA‐MRSA strains tended to be multidrug resistant and less virulent than both LA‐ and CA‐MRSA strains. Importantly, CA‐MRSA strains had a high homology with each of HA‐ and LA‐MRSA. However, no similarity was observed between HA‐ and LA‐MRSA. Our findings suggest that the epidemiological changes in genetic behaviour between HA‐ and LA‐MRSA are due to the presence of CA‐MRSA confirming that CA‐MRSA has created a public health crisis worldwide.