Methicillin-resistant Staphylococcus aureus (MRSA) constitutes a significant health concern because it promotes infectious mastitis in dairy animals and poses a hazard risk to humans. Controlling MRSA infections is a growing challenge on a global scale because of the bacteria's toxicity and its capacity to develop multidrug resistance (MDR). Combating against MDR bacteria and the spread of infectious diseases needs natural antibacterial alternatives to minimize the economic losses of mastitis. The average treatment cost in Egypt was highlighted. The antibacterial effect of apple cider vinegar (ACV) against MDR-MRSA isolates was evaluated, also the study aimed at profiling antimicrobial resistance genes in MRSA isolates. The incidence of mastitis in cows was more than in buffaloes, and the average total treatment cost was estimated at 82 million EGP from 2016 to 2021 (around 14 million EGP annually). Of the 22 S. aureus isolates (20 %), of which (59.1 % were from cows and 40.9 % from buffaloes), 19 (86.4 %) were confirmed as MRSA. All MRSA isolates exhibited resistance to clindamycin (94.7 %), then both ampicillin and doxycycline (84.2 %), and ampicillin and sulbactam, erythromycin and Fosfomycin (each, 78.9 %). Vancomycin, ciprofloxacin, and levofloxacin can be used to treat MRSA. The prevalence of MDR was significantly high, with 94.7 % of the cases having multiple antimicrobial resistance (MAR) indices ranging from 0.25 to 0.75. All MRSA isolates tested positive for mecA, 89.5 % for the blaZ gene, 84.2 % for tetM, and 73.4 % for ermB. In vitro, the antibacterial properties of ACV were demonstrated to be superior by our results which demonstrate a zone of inhibition with diameters ranging from 20 to 40 mm detected by Agar well diffusion technique and MIC's (Minimal Inhibitory Concentration) ranging from 2 to 4 μg/ml. Some isolates possess MBC (Minimal Bactericidal Concentration) values at the same MIC. This research proposes the potential of ACV to act as a promising antibacterial alternative against MRSA. This can help minimize the health problem of antibiotic-resistant bacteria and improve the efficiency of dairy farms. Further studies are recommended to determine the proper dosage for field administration.