To evaluate the molecular epidemiology and to georeference Staphylococcus aureus isolated from wounds and nares of patients seen at Basic Health Units (BHUs) of a Brazilian city. Observational, cross-sectional study conducted from 2010 to 2013. A total of 119 S.aureus strains isolated from the wounds and nares of 88 patients were studied. The isolates were characterised by identifying virulence genes encoding enterotoxins A-E, haemolysins α, β and δ, exfoliatins A, B and D, biofilm production, Panton-Valentine Leukocidin and toxic shock syndrome toxin 1, and by pulsed-field gel electrophoresis (PFGE), multilocus sequence and spa typing. Eighteen methicillin-resistant Staphylococcus aureus (MRSA) (6 SCCmec type II and 12 SCCmec type IV) and 101 (85%) MSSA were identified. PFGE typing resulted in the formation of eight clusters, with STs 1, 5, 8, 30, 188, 1176 and 1635 and spa type t002 being the predominant types among MSSA. The 18 MRSA belonged to STs 5, 8 and 1176 and spa types t002 and t062. The results demonstrate widespread dissemination of MSSA and MRSA clones carrying haemolysin, biofilm and toxin genes. Kernel density estimation revealed the highest density of S.aureus in the 4, 5 and 8 BHUs.