This study emphasizes the importance of monitoring the microbiological quality of animal products, such as raw sheep’s milk and cheese, to ensure food safety. In Brazil, there is currently no legislation governing the quality of sheep’s milk and its derivatives. Therefore, this study aimed to evaluate: (i) the hygienic-sanitary quality of raw sheep’s milk and cheese produced in southern Brazil; (ii) the presence of enterotoxins andStaphylococcusspp. in these products; and (iii) the susceptibility of the isolatedStaphylococcusspp. to antimicrobial drugs and the presence of resistance genes. A total of 35 samples of sheep’s milk and cheese were examined. The microbiological quality and presence of enterotoxins were accessed using Petrifilm and VIDAS SET2 methods, respectively. Antimicrobial susceptibility tests were conducted using VITEK 2 equipment and the disc diffusion method. The presence of resistance genestet(L),sul1,sul2,ermB,tetM, AAC(6)’,tetW, andstrA were evaluated through PCR. In total, 39Staphylococcusspp. were obtained. The resistance genestetM,ermB,strA,tetL,sul1, AAC(6)’, andsul2 were detected in 82%, 59%, 36%, 28%, 23%, 3%, and 3% of isolates, respectively. The findings revealed that both raw sheep’s milk and cheese containedStaphylococcusspp. that exhibited resistance to antimicrobial drugs and harbored resistance genes. These results underscore the immediate need for specific legislation in Brazil to regulate the production and sale of these products.