This study aimed to determine the frequency and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) from Australian animals and whether animal-derived MRSA was similar to that from Australian veterinarians. A total of 1,080 clinical coagulase positive Staphylococcus isolates from Australian animals were collected during 2013. Sixteen (4%) of 360 S. aureus isolates were MRSA. Most MRSA came from companion animals, while none came from livestock. MRSA isolates were characterized using whole genome sequencing. ST22-IV (EMRSA-15) was the most common clone in dogs and cats. Clonal complex (CC) 8 was most common in horses. Most ST22-IV isolates were resistant to ciprofloxacin. Animal-derived MRSA genomes were interrogated for the presence of host-specific genetic markers (staphylokinase gene [scn], chemotaxis-inhibiting proteins gene [chp], staphylococcal complement inhibitor gene [sak], enterotoxin A gene [sea], and Von Willebrand Factor binding protein gene [vwb]). A subset of MRSA genomes previously collected from Australian veterinarians was also interrogated. There was no clear pattern in the distribution of host-specific markers among animal and veterinarian isolates. Animal- and veterinarian-derived MRSA were intermingled in the phylogenetic tree. The absence of MRSA in Australian livestock is in stark contrast with its presence in livestock from other countries. Possible explanations include Australia's geographic isolation, the absence of live animal importation into Australia, and most notably, the restrictions placed on the use of antimicrobials of critical importance in Australian livestock.