Background:  Diarrhoea is an important cause of morbidity and mortality among children in developing countries and resistance of bacteria is a global problem.Objective: The present study in Unguja Island, Zanzibar, aimed at determining the prevalence and identity of pathogenic enteric bacteria associated with diarrhoea in children under five years and to assess the resistance of these bacteria to antibiotics.Methodology: A cross sectional quantitative study was conducted, a total of 319 stool samples were collected. The prevalence and identity of pathogenic enteric bacteria were determined through conventional methods and antimicrobial resistance by the Kirby-Bauer antibiotic testing method.Results: The prevalence isolates were; Shigella spp. In 41.5%, Salmonella spp.(29.3%), Vibrio parahaemolyticus(13.1%) and pathogenic E. coli (16.2%). Pathogenic enteric bacteria were commonly more resistant to sulfamethoxazole/trimethoprim, Erythromycin, Tetracycline and Ampicillin but were less resistant to Ciproflaxin, Gentamycin, and Chloramphenicol respectively.Conclusion: The results indicated that the prevalence of pathogenic enteric bacteria was high and often they were resistant to antibiotics commonly used to treat diarrhoea in children under five years in Zanzibar. We therefore recommend reviewing of guidelines for treatment of childhood diarrhoea, promote health education, scale up vaccination campaign and regulate the use of antimicrobials to prevent further development of antibiotic resistance.