Background: Subclinical mastitis is the most underrated yet economically important disease of livestock. It goes undetected by clinical examinations, making routine surveillance and monitoring necessary for its detection. Among causative agents, Staphylococcus aureus is the most crucial one. The present study determines the prevalence, antimicrobial resistance profile and molecular characterization of S. aureus from subclinical mastitis of cattle in the Mathura region. Methods: The present research was conducted during 2019-2021 and different gaushalas and dairies in and around the Mathura region were screened for mastitis by California mastitis test and somatic cell count. The samples positive were further tested by bacterial, biochemical and molecular tests along with an antimicrobial resistance profile. Result: Our research found a significant amount of S. aureus in subclinical samples with the presence of mecA gene suggesting MRSA. The public health importance of S. aureus and emerging resistance against antibiotics demands regular monitoring and effective use of antimicrobial agents against the MRSA isolates.