Objective To explore the whole-genome characteristics of methicillin-resistant Staphylococcus aureus （MRSA）.Methods Four ST9 MRSA strains isolated from pig carcasses and slaughter workers were collected and sequenced. The genetic characteristics， resistance genes and virulence genes of their genomes were analyzed. Single nucleotide polymorphism（SNPs） were screened by comparative genomics， and the comparisons with the core genes of 11 MRSA and methicillin sensitive Staphylococcus aureus（MSSA） with different ST type from NCBI were analyzed to construct a phylogenetic tree.Results The results showed that the full-length genomic sequence of the four ST9 MRSA strains from different sources was about 2.6 Mbp， of which contained 2 122-2 494 genes， and the average GC content of the genes in the four genomes was 32.8%. The genomes from different sources contained 26-31 drug resistance genes and 44-56 virulence genes. Compared with ST398 MRSA which was popular in Europe and other countries， the four ST9 MRSA strains had high nucleotide homology， and the numbers of SNPs between strains were less than 300. The phylogenetic tree analysis showed that ST9 and ST398 MRSA had been divided into different independent evolutionary branches in the molecular evolutionary courses. MRSA strains from animal and human origin had no obvious correlation in molecular evolution.Conclusion This study obtained background materials on the basic characteristics of the ST9 MRSA genome from different sources， which could help understand the molecular evolutionary traceability of different ST-type MRSAs. These data will provide scientific guidance for subsequent studies on the molecular epidemiology and pathogenic mechanism of ST9 MRSA.