Methicillin-resistant Staphylococcus aureus (MRSA) clones belonging to the Brazilian, Pediatric, Cordobes/Chilean and New York/Japan clonal complexes are widely distributed across Latin America, although their individual distribution patterns and resistance to antimicrobial drugs are constantly changing. Furthermore, clones with increased virulence are beginning to appear more frequently both in hospital and community settings, and there is evidence that virulence factors can be transferred between hospital- and community-associated clones through recombination. These changing patterns have significant implications for clinical practice in the region. Most importantly, clinicians need to be aware of the changing antimicrobial resistance profile of circulating MRSA clones in their region in order to choose the most appropriate empiric antimicrobial therapy. Thus, regional molecular epidemiology programs are required across the region to provide accurate identification and characterization of circulating MRSA clones.