The current study aims to use coagulase (coa) polymorphism gene to identify Staphylococcus aureus isolated from stool samples, evaluate the efficiency of these methods in discriminating variable strains, and compare these subtypes with antibiotypes. A total of 100 specimens were collected from patients in Babylon province, Iraq, between July 2016 and September 2016. Twenty S. aureus strains were isolated and identified using standard laboratory microbiological tests. The bacterial isolates were then examined by coa gene restriction fragment length polymorphism genotyping. Out of 20 isolates, coa gene types were classified, and the amplification products showed multiple size bands (500, 600, 700, 800, and 900-bp bands). Coa gene PCR restriction fragment length polymorphisms exhibited seven patterns that ranged from one to four fragments with AluI digestion. The results have demonstrated that many variants of the coa gene are present. At least one type of S. aureus newly described enterotoxin gene (staphylococcal enterotoxins) was harboring in all 20 (100%) of the isolates. The most frequently encountered gene were sei (100.%), seh (5%), seg (65%). Many S. aureus isolates carry at least one of the enterotoxin genes, and (95%) strains harbored more than one toxin gene coding.