The microbial count in fresh milk of healthy ewe is low. However, contamination occurs during milking, handling, transportation, and processing. Therefore, in this study, udder surface, milk and some cheese samples were examined for bacteriological (total plate count, Enterobacteriaceae, E. coli, and S. aureus, psychrotrophic and lactic acid bacteria) counts. Furthermore, determination of the coefficient of correlation between the major bacterial counts; California Mastitis test (CMT); and staphylococcal and lactic acid bacteria strains were characterized. CMT score was recorded only in 16 (12.9%) udder half milk samples. The overall total plate count mean value was 2.5 ± 0.8 lg CFU/cm2, 3.1 ± 1.1, and 7.0 ± 0.9 lg CFU/mL in udder surface, individual raw and bulk tank milk (BTM) samples, respectively. In the case of Enterobacteriaceae count, the overall mean value was 1.2 ± 0.7 lg CFU/cm2, 1.9 ± 0.8 and 5.1 ± 0.9 lg CFU/mL in udder surface, individual raw and BTM samples, respectively. Enterobacteriaceae count value were ranged from 0.0 ± 0.0 to 5.5 ± 0.2 lg CFU/g in cheese samples. E. coli was not detected in any of udder surface and individual raw milk samples. E. coli count in chives-flavoured and garlic-flavoured-smoked cheese samples failed to meet regulatory standards. S. aureus was detected in only two udder surface (2.6%) and six individual raw milk samples (7.0%). S. aureus was detected in only two BTM (20%) samples of Farm III. S. aureus count mean value was 5.7 ± 0.2 lg CFU/g in chives-flavoured cheese and not detected in the other cheese types. Psychrotrophic bacteria count was 4.3 ± 1.0 and 3.6 CFU/mL in BTM samples of Farm III and IV respectively. Lactic acid bacteria count in BTM obtained from Farm III and IV was 6.7 ± 0.4 and 4.2 lg CFU/mL, respectively. The mean of lactic acid bacteria count was 7.5 ± 0.1 and 6.5 ± 0.3 lg CFU/g in garlic-flavoured-smoked cheese and garlic-flavoured cheese, respectively. Weak to moderate positive correlations were observed between the bacterial count pairs evaluated. Four bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) were present in milk samples analysed for microbiota taxonomic profile. Furthermore, the resistance against tetracycline was observed in six S. aureus, and penicillin G, tetracycline, trimethoprim/sulfamethoxazole, and erythromycin resistance was detected in at least one of five resistant coagulase-negative staphylococci strains. Eight lactic acid bacteria strains were resistant to at least one of the two antibiotics (cefoxitin and tetracycline). Also, SE genes were detected in 25 S. aureus and one coagulase-negative Staphylococcus strains in which SEC was the most prevalent, being detected in 17 S. aureus strains.