Abstract: Background and Objective: The emergence of methicillin-resistant Staphylococcus aureus in animals has been an outbreak of mastitis in cattle which represents a great economic loss in milk industry and a serious public health concern worldwide. The objective of this study was to identify the antimicrobial resistance patterns and the prevalence of methicillin resistant and susceptible Staphylococcus aureus harboring the classical staphylococcal enterotoxin genes in bovine mastitis cases. Materials and Methods: A total of 112 Staphylococcus aureus isolates were investigated for antibiotic resistance patterns. Some of the isolates were subjected to genotypic analysis for methicillin-resistant genes (mecA) and classical staphylococcal enterotoxin A through E genes. Results: Methicillin-resistant Staphylococcus aureus was phenotypically detected in 77 (68.7%) of the isolates, while methicillin-susceptible Staphylococcus aureus was identified in 35 (31.2%) of isolates, most of the isolates were showed multidrug-resistance to at least one member of the antimicrobial classes. By genotypic analysis, 54.5% phenotypically methicillin-resistant isolates were mecA gene positive (methicillin-resistant Staphylococcus aureus), while 45.5% of the isolates were mecA gene negative (methicillin-susceptible Staphylococcus aureus). Variation in the staphylococcal-enterotoxin encoding genes was detected. The 66.7% of methicillin-resistant Staphylococcus aureus and 80% of methicillin-susceptible Staphylococcus aureus were encoding staphylococcal enterotoxin genes. The most frequently detected staphylococcal enterotoxin genes were the combination of staphylococcal enterotoxin A, D and E representing 50% of methicillin-resistant Staphylococcus aureus isolates as well as staphylococcal enterotoxin D representing 75% of methicillin-susceptible Staphylococcus aureus isolates. Conclusion: The high prevalence of multidrug-resistant and toxigenic methicillin resistant and susceptible Staphylococcus aureus strains in bovine milk are considered as a potential threat to public health. Hence, the right use of antibiotic of choice in the line of treatment and control of the bovine mastitis caused by Staphylococcus aureus is very crucial in Egypt.