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Abattoir workers have been identified as high-risk for livestock-associated <i>Staphylococcus aureus</i> carriage. This study investigated <i>S. aureus</i> carriage in abattoir workers in Western Kenya. Nasal swabs were collected once from participants between February-November 2012. <i>S. aureus</i> was isolated using bacterial culture and antibiotic susceptibility testing performed using the VITEK 2 instrument and disc diffusion methods. Isolates underwent whole genome sequencing and Multi Locus Sequence Types were derived from these data. <i>S. aureus</i> (<i>n</i> = 126) was isolated from 118/737 (16.0%) participants. Carriage was higher in HIV-positive (24/89, 27.0%) than HIV–negative participants (94/648, 14.5%; <i>p</i> = 0.003). There were 23 sequence types (STs) identified, and half of the isolates were ST152 (34.1%) or ST8 (15.1%). Many isolates carried the Panton-Valentine leucocidin toxin gene (42.9%). Only three isolates were methicillin resistant <i>S. aureus</i> (MRSA) (3/126, 2.4%) and the prevalence of MRSA carriage was 0.4% (3/737). All MRSA were ST88. Isolates from HIV-positive participants (37.0%) were more frequently resistant to sulfamethoxazole/trimethoprim compared to isolates from HIV-negative participants (6.1%; <i>p</i> < 0.001). Similarly, trimethoprim resistance genes were more frequently detected in isolates from HIV-positive (81.5%) compared to HIV-negative participants (60.6%; <i>p</i> = 0.044). <i>S. aureus</i> in abattoir workers were representative of major sequence types in Africa, with a high proportion being toxigenic isolates. HIV-positive individuals were more frequently colonized by antimicrobial resistant <i>S. aureus</i> which may be explained by prophylactic antimicrobial use.