Background: Surgical site infections are related to high morbidity, mortality and healthcare costs. Because the emergence of multidrug-resistant bacteria in hospitals is becoming a worldwide challenge for surgeons who treat healthcare-associated infections, we wished to identify the causative agents involved in these infections and the rate of multidrug-resistant bacteria in six public hospitals in Benin. Methods: Using standard microbiological procedures, we processed pus specimens collected from obstetrics and gastrointestinal surgery wards. Mass spectrometry (MALDI-TOF) was used for confirmation. For the antibiotic susceptibility test, we first used the Kirby-Bauer disk diffusion method. The secondary test (by microdilution) used the Beckton Dickinson Phoenix automated system (Becton Dickinson Diagnostic, USA). Results: We included 304 patients, whose median length of stay was 9 days. A total of 259 wound swabs (85.2%) had positive aerobic bacterial growth. In obstetrics, S. aureus (28.5%, n=42) was the most common isolate. In contrast, Gram-negative bacteria (GNB) were predominant in gastrointestinal surgery, the most dominant being E. coli (38.4%, n=31). Overall, 90.8% (n=208) of aerobic bacteria were multidrug resistant. Two-thirds of S. aureus (65.3%, n= 32) were methicillin-resistant Staphylococcus aureus (MRSA), three of which carried both MRSA and induced clindamycin resistance (ICR). GNB showed high resistance to ceftazidime, ceftriaxone and cefepime. Extended-spectrum beta-lactamases were presented by 69.4% of E.coli (n=43/62) and 83.3% of K. pneumoniae (n=25/30). Overall, twelve Gram-negative bacteria (5.24%) showed resistance to at least one carbapenem. No isolates showed a wild-type susceptible phenotype. Conclusion: This study shows the alarming prevalence of multidrug-resistant organisms from surgical site infections in Benin hospitals. To reduce the spread of such bacteria, periodic surveillance of surgical site infections and strict adherence to good hand-hygiene practice are essential.