The emergence of novel pathogens poses a major threat to public and veterinary health. Staphylococcus aureus is a multi-host bacterial pathogen and a leading cause of antibiotic resistance–associated mortality worldwide. Although widely recognized as a human pathogen, its evolutionary history is shaped by frequent host-switching between humans and livestock, driving the emergence of distinct pathogenic clones in different host populations. In this presentation, I will trace the evolutionary origins of major contemporary S. aureus lineages causing disease in humans and livestock, and examine their spatial and temporal dynamics. I will highlight how different types of evolutionary events have contributed to infection niche adaptation. Our analyses reveal substantial variation among lineages in pangenome size, structure, and gene flow, influenced by both genetic constraints and ecological barriers to HGT. Notably, pangenome openness varies markedly across lineages and correlates strongly with host-species promiscuity. We further show that lineages are structured by horizontally acquired defense systems, with divergence among subpopulations linked to variation in type I restriction–modification (R–M) system repertoires. Together, these findings demonstrate that HGT of defense systems is a key driver of S. aureus lineage diversification, while host ecology plays a central role in shaping accessory genome variation.