The extensive use of antibiotics created two of the biggest hazards to global health in the twenty-first century, namely, antibiotic residues and antimicrobial-resistant (AMR) bacteria. This research seeks to scrutinize the correlation between antibiotic residues and antibiotic-resistance genes (ARGs) of Staphylococcus aureus (S. aureus). 120 raw milk samples were systematically procured from diverse sources, involving dairy farms (40), farmers' houses (20), dairy shops (40), and street vendors (20). These samples underwent thorough screening for subclinical mastitis (SCM), S. aureus counts, and antibiotic residues. Coagulase-positive S. aureus (CPSA) was isolated and quantified in 15% (18/120) of the samples. Among these isolates, 94.4% displayed resistance to penicillin, 5.6% to trimethoprim, 22.2% to gentamycin, ofloxacin, and erythromycin, while 27.8% exhibited resistance to vancomycin. PCR amplification of 23S rRNA confirmed the identity of all tested strains as S. aureus (100%), which were then found to harbor ARGs associated with β-lactams (blaZ gene), aminoglycosides (aac(6')aph (2'') gene), and vancomycin (Van A gene). Milk samples that underwent reverse-phase high-performance liquid chromatography (HPLC) revealed residues of oxytetracycline, amoxicillin, and gentamicin at rates of 8.3%, 1.7%, and 6.7%, respectively, with maximum levels exceeding the European Union Maximum Residue Limits (EU-MRL) (2010). The ARGs related to multidrug-resistant (MDR) S. aureus were identified in 40% (8/20) of milk samples contaminated with antibiotic residues.