Staphylococcus are common bacteria that can be a component of the natural microbiota of the body of human and animal hosts or cause serious infections. The aim of this study was to analyze the presence of S. aureus in samples from two sheep breeds (Świniarka and Uhruska), assess the antimicrobial susceptibility and virulence profile of these microorganisms, and perform molecular comparative analysis of these bacteria. One hundred and three isolates of S. aureus strains were obtained (including five MRSA strains) and the highest phenotypic resistance to tetracycline (46.6%), clindamycin (45.6%), erythromycin (39.8%), and penicillin (31.1%) was confirmed. The tetL gene (27.2%) and the seB gene (44.7%) were the most frequently detected in strains. Three new sequence types in the MRSA isolates (ST 9313, ST 9314, ST 9315) were identified. In conclusion, our results confirm that sheep are significant reservoirs of S. aureus, especially MRSA strains, varying in terms of both resistance and virulence and with the potential to spread between individuals in the same herd, which may pose a potential health problem.