The objective of this study was to assess the prevalence, antimicrobial susceptibility, and distribution of virulent genes in Staphylococcus aureus (S. aureus) and MRSA isolates from healthy sheep and goats, as well as their shepherds. The study included 50 sheep, 50 goats, and 32 shepherds. Three types of samples were collected from each animal - milk samples, nasal swabs, and rectal skin swabs, while the shepherds provided thirty-two nasal swabs and 32 hand swabs. Biochemical tests were used to identify S. aureus colonies, and cefoxitin disk diffusion was employed to identify MRSA isolates. The isolates were then tested for nuc, mecA, PVL, and VanA genes. S. aureus was detected in 84.20% of the tested sheep samples, 51.33% in goats and 84% among shepherds. MRSA was present in 54% of milk samples, 58% of nasal swabs, and 48% of skin swabs in sheep. In goats, MRSA was found in 59%, 42%, and 58%, respectively. In shepherds, MRSA isolates were detected in 88% of nose swabs and 90% of hand swabs. All MRSA isolates were multi-drug resistant, with penicillin G showing the highest resistance (100%). In conclusion, sheep, goats, and their shepherds, may play a significant role in the transmission of S. aureus. Moreover, the presence of MRSA in raw milk, nose swabs, and skin swabs may contribute to the spread of the bacteria to other individuals.