Background: Surgical site infection (SSIs) is one of the most common healthcare-associated infections. It comprises a great risk to hospitalized patients in terms of morbidity, mortality and economic cost. Objectives: To identify the causative organism(s) responsible for surgical site infection following Cesarean section and to trace the source of that infection. Patients & methods: A total of 623 clinical samples and swabs were collected from Obstetrics & Gynecology Department at Al-Zahraa University Hospital. The study included 300 patients with provisional diagnosis of SSI from whom, wound swabs were taken, in addition to 23 swabs from medical staff and 300 environmental samples. Samples were subjected to conventional bacteriological identification, biochemical reactions, antibiogram and genotyping by Random Amplified Polymorphic DNA (RAPD) assay of the dominated isolates. Results: Out of 300 wound swabs from patients with SSI following CS surgery, 62 (20.7%) yielded aerobic microbial growth. Eighty three out of 323 swabs (26%) collected from health care workers (HCWs) & environment were positive on culture. The most common organism isolated from both sources (clinical & environmental specimens) was Methicillin resistant Staphylococcus aureus (MRSA) isolates 35/623 (5.6%). Genotyping of MRSA isolates revealed 20 distinct Random Amplified Polymorphic DNA (RAPD) patterns, indicating high rate of genetic heterogeneity among MRSA isolates. Conclusion: There were clonally related MRSA isolates obtained from operating room and from patients, indicating that the operating room was accused as a source of infection.