Staphylococcus aureus is a common microflora present on skin and mucous membrane of cattle. Despite its amiable nature, S. aureus can turn shrewd and get to be distinctly pathogenic. Staphylococcus present in the milk may produce numerous potential destructive variables, like toxins. Consequently, consumption of S. aureus contaminant milk may result in Staphylococcal food poisoning (SFP). Therefore, the present study was carried out to evaluate the presence of Se-encoding genes in S. aureus and also validate the detection of toxin genes directly from the milk sample contaminated with S. aureus using real-time polymerase chain reaction (RT-PCR). The RT-PCR results were reported as Ct values, which confirmed the presence of enterotoxin genes in the S. aureus isolates and milk samples. Application of RT-PCR for the detection of Se genes in cultures of S. aureus and also from milk samples revealed the probable onset of SFP. Therefore, the study suggests that the analysis of milk for the presence of any toxin genes should be strictly performed before reaching the consumer.