Staphylococcus aureus is a widespread and common opportunistic bacterium that cancolonise or infect humans as well as a wide range of animals. There are a few studies of bothmethicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolated frommonkeys, apes, and lemurs, indicating a presence of a number of poorly or unknown lineagesof the pathogen. In order to obtain insight into staphylococcal diversity, we sequenced strainsfrom wild and captive individuals of three macaque species (Macaca mulatta, M. assamensis, andM. sylvanus) using Nanopore and Illumina technologies. These strains were previously identifiedby microarray as poorly or unknown strains. Isolates of novel lineages ST4168, ST7687, ST7688,ST7689, ST7690, ST7691, ST7692, ST7693, ST7694, ST7695, ST7745, ST7746, ST7747, ST7748, ST7749,ST7750, ST7751, ST7752, ST7753, and ST7754 were sequenced and characterised for the first time. Inaddition, isolates belonging to ST2990, a lineage also observed in humans, and ST3268, a MRSA strainalready known from macaques, were also included into the study. Mobile genetic elements, genomicislands, and carriage of prophages were analysed. There was no evidence for novel host-specificvirulence factors. However, a conspicuously high rate of carriage of a pathogenicity island harbouringedinB and etD2/etE as well as a higher number of repeat units within the gene sasG (encoding anadhesion factor) than in human isolates were observed. None of the strains harboured the genesencoding Panton–Valentine leukocidin. In conclusion, wildlife including macaques may harbour anunappreciated diversity of S. aureus lineages that may be of clinical relevance for humans, livestock,or for wildlife conservation, given the declining state of many wildlife populations.