In this study, 164 milk samples (60 clinical, 44 subclinical, 60 healthy) were collected from mastitic cattle and buffaloes 82 samples for each. Using California mastitis test 130/164 (79.26%) were confirmed to be from mastitic cases. A total of 59 Staphylococcus spp. isolates were identified and distributed as following; 25/82 (30.4%) from mastitic cattle,10 from clinically mastitic cases,12 isolates from subclinical cases and 3 isolates from healthy cases. Moreover, 33/82 (40.24%) were isolated from mastitic buffalo, 15 from clinical cases, 14 from subclinical cases and 5 from healthy cases. Most of the obtained isolates were phenotypically confirmed to be Methecillin resistant Staphylococcus aureus (MRSA). From the 13 applied antimicrobials Vancomycin, Doxycycline, Ciprofloxacin, Norfloxacin, and Gentamycin were the most effective with the following rates; 75%, 50%, 50%, 50%, and 45% respectively.With molecular confirmation, genes responsible for resistance to methicillin were mecA, A1, A2, mecA1, and mecC with the following rates; 58.3%, 50 %, and 91.7% while the blaZ gene responsible for resistance to pencilline represented 66.7%.