Staphylococcus aureus is commonly associated with mastitis in dairy herds with potential public health implications. Overall, 303 samples were collected from September 2015 to July 2016 to characterize the phenotypic and genotypic pattern of drug resistance in S. aureus isolated from cases of clinical and sub-clinical bovine mastitis in Central Ethiopia. Milk samples were tested by using California Mastitis Test and positive samples were subjected for bacterial culture, disc diffusion test and polymerase chain reaction (PCR) to detect the presence of antimicrobial resistance. Based on California mastitis test (CMT) result and clinical examination, the prevalence of mastitis was 70.6%. S. aureus was isolated from 36.9% of CMT positive samples. The phenotypic determination of antimicrobial resistance showed that the isolates were most resistant to ampicillin (80%) followed by trimethoprim-sulfamethoxazole (23.3%), tetracycline (15%), streptomycin (10%) and gentamycin (3.3%) and equally to both erythromycin and chloramphenicol (1.6%). Characterization of the antimicrobial resistance gene was done by using PCR. Most of the isolates (56%) contained blaZ gene followed by ermB (33%), ermC (13.3%) and each ermA and msrA appeared only in 2% of the isolates. There was no isolate harboring the methicillin resistance mecA gene. Thirty six percent of the isolates contained more than one antibiotic resistance genes. The highest multidrug resistance (MDR) gene combination was observed by blaZ*ermB (31.25%) genes and the least frequently occurred were blaZ *ermA and msrA*ermB (3.12%) each. This study showed that consumption of raw milk could be considered as a critical source of antibiotic resistant S. aureus.