The problems on identificationof Staphylococcus aureus isolatesfrom cheese samples were investigated by phenotypic and genotypic tests in thisstudy. Among 207 Staphylococcus spp. isolated from 31 cheese samples, 23isolates that were Gram positive, catalase and slide coagulase positive, with 1isolate that was latex agglutination test negative showed different phenotypicproperties. Polymerase chain reaction (PCR) and quantitative PCR (qPCR)analyses showed that DNase test and target genes (nuc, coa) regarded asgold standard regions for S. aureuswere not found to be unique for identification of S. aureus. The toxin genes (SEA-SEE) were not detected by PCR.Antibiotic resistance profiles of S.aureus isolates demonstrated that two isolates were resistant to penicillinG. This study showed that the unique phenotypic and genotypic test was notadequate for identification of S. aureusisolates. There was no correlation between the presence of the nuc gene and toxin genes. The presenceof nuc gene which was used fordetection of S. aureus was also foundto be present in other Staphylococcusisolates. As a conclusion, the results revealed that biochemical tests couldlead to false positive results for identification of S. aureus. The presence of nucgene is not correlated with the presence of toxin genes.