Pathogenic strains of Staphylococcus aureus can cause disease in both humans and animals. In animal species, including ruminants, S. aureus is capable of causing severe mastitis and sub-clinical mastitis. Animals with mastitis frequently shed S. aureus into the milk supply which can result in food poisoning in humans. The aim of this study was to use typing methods including pulsed field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and enterotoxin profiling to understand the diversity of S. aureus isolates from seven dairy farms in Victoria. A survey of 120 samples collected from three bovine, two caprine and two ovine dairy farms yielded 13 isolates of S. aureus from milk and milk filter samples. Caprine and ovine isolates shared greater than 80% similarity regardless of source using PFGE. Conversely, bovine isolates were shown to be of much greater diversity. MLST of the bovine isolates found sequence types (STs) of both human and ruminant origin. In contrast, all caprine and ovine isolates belonged to ST133, this has been observed in small ruminants from other countries. Staphylococcal enterotoxin (SE) profiling indicated caprine and ovine isolates possessed 1-3 different SEs, whereas bovine isolates carried between 1-9 SEs. This study indicates that S. aureus from ruminant animals are varied; however, dominant STs may exist within particular animal types. Gaining an understanding of the genotypic diversity that exists within Australian S. aureus isolates may assist the development of future treatment strategies.