Staphylococcus aureus (S. aureus) is one of the most common pathogens causing both human and animal infections. Transmission of S. aureus to humans via contaminated food continues to be a health public concern. In the present study, 104 strains including eight MRSA strains were identified from 507 chicken samples (20.5%) in three cities of China. These strains harbored the highest resistance against penicillin (91.4%), followed by tetracycline (64.4%), erythromycin (53.5%), and kanamycin (32.7%). We used spa typing to classify these isolates into 28 types belonging to two lineages including the predominant type t112 (n = 26) and four newly identified spa types. Among the 104 strains, six carried the CRISPR-Cas system, a prokaryotic immune system which protects against foreign genetic elements. Interestingly, rpoB gene sequencing demonstrated that these six initially designated ST2250 strains were in fact S. argenteus, a novel Staphylococcus species genetically closely related to S. aureus. Three Staphylococcus CRIPSR types containing ten spacers identified in these strains have been reported in CRISPR-positive S. aureus. Additionally, 80% of the spacers showed homology to S. aureus phages demonstrating that these conserved spacers were closely related to the phages in the environment of S. argenteus. We speculated that the identical CRISPR types and spacers in both S. argenteus and S. aureus have resulted via exchange of mobile elements between these two species. Emergence of food-borne ST2250 S. argenteus is a potential threat to human public health.