Abstract: Background and Objective: Fish is a highly desirable foodstuff as it possesses excellent nutritional components, it is man’s most important source of high-quality protein. Fish supplies, however, are dwindling due mainly to pollution of the aquatic environment. Toxicants enter fish, they affect fish organs, bioaccumulate and invariably affect the end consumer of such contaminated fish. This study aimed at identifying the bacterial flora present in the gut and gills of Oreochromis niloticus and Clarias gariepinus. Materials and Methods: This research was conducted to assess the bacterial load on fish species found in Ureje Reservoir in Ekiti State. The most popular freshwater fish species in Ureje Reservoir are Oreochromis niloticus and Clarias gariepinus. Samples of each fish species were kept in sterile bags and transported to the laboratory for bacterial analysis. Results: Eight bacteria species were identified (Staphylococcus aureus, Salmonella typhimurium, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumonia, Proteus spp., Enterococcus spp. and Streptococcus spp.). The highest colony count was found in the gut of Clarias gariepinus. The presence of these bacteria species could pose a potential public health threat to consumers. Conclusion: It is recommended that better handling and processing methods should be adopted to eliminate health risks to fresh fish consumers.