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Hard and semi-hard cheeses are popular dairy products in Egypt, but they may convey a health risk for consumers due to their poor hygienic quality and safety. One of the common problems that consumers face when buying these cheeses from the Egyptian market is the bad odour that shortly develops after purchase even though they are refrigerated. This problem may indicate a high bacterial count in the cheese or the presence of undesirable microorganisms. Therefore, the current study aimed to assess the hygienic quality and safety of some retailed cheese sold in Egyptian markets. One hundred hard and semi-hard cheese samples locally manufactured (including 34 Ras, 33 Cheddar, and 33 Gouda) were analyzed for their microbiological and chemical quality. The results indicated that the Ras cheese samples had the highest bacterial counts, salt, and fat content, while the Cheddar cheese samples had the highest acidity, moisture content and the lowest microbial load. The Gouda cheese samples had the lowest fat/total solids ratio and a variable bacterial count. Forty-five Staphylococcus aureus strains were isolated from the cheese samples; 25 of them were coagulase-positive. The antibiotic susceptibility of twenty isolates was phenotypically and genotypically evaluated. All isolates were resistant to Cefixime, Oxacillin, and Metronidazole, while sensitive to Amoxicillin/Clavulanic Acid and Linezolid. The resistance to other antibiotics varied among the isolates. The antibiotic resistance genes were detected by polymerase chain reaction (PCR). The obtained results indicate that the hard and semi-hard cheeses sold in many markets were poor in hygienic quality and safety and posed a health risk for consumers due to the presence of multidrug-resistant Staphylococcus species. Ras cheese was the worst cheese type in most quality and safety parameters.