BACKGROUND: Methicillin resistant Staphylococcus aureus (MRSA) is one of the main causes of hospital-acquired infections, but the diagnosis of MRSA pseudomembranous enteritis has faded in recent years. Here, we reported a pseudomembranous enteritis case in a young male patient caused by ST5 MRSA. METHODS: Clinical data of the patient were collected from medical records. Mass spectrometry identification, antimicrobial susceptibility testing, whole genome sequencing, as well as resistance and virulence genes detection of MRSA strain were performed. RESULTS: A 27-year-old young man with acute pancreatitis and septic shock in the intensive care unit passed large volume of intestine-like "stool" with more than 200 centimetres in length. A large number of Gram-positive cocci was persistently found in the stool samples. Histopathological examination of the intestine-like stool revealed that this stool was actually pseudomembrane, consisting of fibrinous exudate, inflammatory cells and clusters of gram-positive cocci adjacent to the luminal border. The patient was suspected for diagnosis of pseudomembranous enteritis. Stool and gastric juice cultures were positive for MRSA. These strains belonged to ST5-SCCmec II-t311, and harbored abundant virulence genes, especially enterotoxin genes. They contained not only sea, sec3, sel, but an enterotoxin gene cluster (egc, seg, sei, sem, sen, seo, yent1 and yent2), which may serve as an enterotoxin gene nursery. Besides, the strains were related to the isolates of the same hospital between 2013 and 2015, and there may be nosocomial transmission. CONCLUSIONS: The severe clinical symptoms in this patient and the described virulence genes all suggested that these ST5 strains belonged to a kind of hypervirulent MRSA lineage. At the same time, the analysis of cgMLST indicated that there might be nosocomial transmission, which required the society to pay more attention to this highly virulent nosocomial clone.