Methicillin-resistant Staphylococcus aureus (MRSA) have been a major cause of healthcare-associated (HA) infection globally for several decades. During this time many distinct clones have emerged independently around the world, some of which have achieved pandemic status. More recently, community-associated (CA) and livestock-associated MRSA clones have also emerged, some of which have become established in hospitals and other healthcare facilities, and sometimes have displaced previously predominant HA clones. Importantly, MRSA can frequently exhibit resistance to a wide range of clinically relevant antibiotics, which limits treatment options and complicates patient management and outcomes. Investigating routes of transmission and spread of MRSA in healthcare facilities have conventionally been undertaken by combining available epidemiological information with data from DNA-based typing systems such as pulse-field gel electrophoresis typing, spa typing, multilocus sequence typing, and more recently, DNA microarray profiling. However, these approaches can frequently lack the discriminatory ability to differentiate between MRSA isolates in healthcare environments where a relatively small number of clones may predominate. The advent of high-throughput whole genome sequencing (WGS) over the last decade with the development of affordable, easy-to-use benchtop DNA sequencing platforms, associated sequencing chemistry and bioinformatics tools, has revolutionized studies of MRSA epidemiology and evolution. The significantly enhanced discriminatory power and resolution afforded by WGS has also provided hitherto unimaginable insights into the origins, emergence and factors that drive the evolution of specific MRSA clones. Furthermore, WGS has highlighted the very significant contributions of mobile genetic elements (MGEs) encoding virulence factors and resistance genes from coagulase-negative staphylococcal (CoNS) species to the emergence and evolution of MRSA. This Research Topic brings together a collection of original research articles and up-to-date reviews that highlight the significant impact WGS is having on our understanding of the epidemiology and routes of transmission of HA- and CA-MRSA in humans and the phylogenetics and evolution of specific MRSA clones. The Research Topic also highlights the impact that WGS is having on our understanding of antimicrobial resistance in MRSA by acquisition of MGEs and the role of specific CoNS species in the origins and evolution of particular MGEs that can promote the survival of MRSA following acquisition. Finally, the Research Topic highlights the immense potential impact of WGS technology in surveillance, rapid pathogen detection, identification of virulence factor profiles and antibiotic resistance genotypes, possibly from clinical samples directly.