Staphylococcus aureus (S. aureus) is emerging as multiple drug resistant (MDR) pathogens in milk of camels with characteristically zoonotic potential. Current study was planned to investigate epidemiology of MDR S. aureus in camel milk, and in-vitro therapeutic response to drugs. Two different ecological zones, Cholistan (n=185) and Suleiman Range (n=177) of Pakistan having major population of camel were screened for subclinical mastitis using California mastitis test using convenient sampling technique. Biochemical examination was performed to isolate S. aureus that further were tested Penicillin, Glycopeptide, and Cephalosporin classes of antibiotics for confirmation of MDR isolates using disk diffusion method. MDR were tested in vitro for response against various antibiotics. A questionnaire was filled for estimation of association of assumed risk factors with prevalence. Nonparametric tests at 5% probability were applied to check significance of results. The study noted overall 33.98% (123/362) of MDR S. aureus from subclinical mastitis milk samples while 123 of 192 S. aureus isolates (64.06%) were confirmed MDR. Non-significantly higher prevalence of MDR was noted in Cholistan area (38.38%) than to that of Sulaiman Range (29.98%) on subclinical mastitis samples basis Similarly 66.36% of S. aureus isolates from Cholistan area and 61.18% from Suleiman Range were presented themselves as MDR. Oxacillin, Cefoxitin and Ampicillin faced 100% resistance while Vancomycin, Cefixime and Cefotaxime had >78 % of resistance from MDR isolates from both study areas. However, Trimethoprim and Ciprofloxacin were > 90%, Chloramphenicol >69%, and Gentamycin 61-67.3%, Streptomicin 61-73.07% and Oxytetracycline 69-71.15%, Enoxacin 45.07 and 53.84% and Amikacin 43.6 and 51.92 effective against MDR. Older age of animals, higher California mastitis score, weak body condition, higher milk yield, early lactation, teat injury, higher parity number, tick infestation, self-treatment and higher use of penicillin in general ailments had positive association with MDR prevalence. The study concluded higher prevalence of MDR S. aureus in camel milk with significant association of assumed risk factors and some of antibiotics presented higher scope of treatment.