Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 9 (ST9) is a potential source of zoonotic infection for humans. In this study, we investigated and compared the virulence profiles of MRSA ST9 isolates from healthy swine and human clinical origins. A total of 152 MRSA ST9 isolates, including 147 LA-MRSA isolates and 5 human clinical isolates, were studied for the accessory gene regulator (agr) and 20 enterotoxin genes (se), exfoliatoxin gene, and tst gene. The evolutionary history of staphylocoagulase (SC) in Taiwan MRSA ST9 was reconstructed based on phylogenetic and population genetics. The predominant type of LA-MRSA ST9 isolates (78.9%) was agr-II that differed from the predominant agr-I human clinical MRSA strains in Taiwan and the LA-MRSA ST398 lineage from Europe. Forty-nine percent of the LA-MRSA ST9 isolates carried a combination of enterotoxin gene cluster-2 (egc-2, seg, sei, sem, sen, seo, and seu) and tst. In addition, the Taiwan LA-MRSA ST9 and the human clinical ST9-MRSA contained a novel SC XIc subtype and had a unique history of evolution indicating a recent common ancestor. These findings suggest a cross-species transmission of this emerging ST9-SC XIc MRSA between swine and human.