Aquaculture in Kenya is progressively developing as an alternative means of human food production and subsistence. An enormous loss in aquaculture has been accelerated by the mortality of Nile Tilapia (Oreochromis niloticus) and African catfish (Clarias gariepinus) fingerlings. This study aimed at screening the internal and external bacteria found in farmed Nile tilapia and African Catfish at Egerton University agro-science fish farm. The microbiology laboratory collected and processed fifteen healthy fish and fish feeds (formulated and commercial). The skin, gills, and intestines were processed and cultured in Salmonella Shigella and Blood agar. Commercial and formulated fish feeds were also processed and cultured in Salmonella Shigella and Blood agar. The resulting bacteria colonies were subjected to morphological examination and biochemical tests for identification. The findings of this study demonstrated the existence of Enterobacteriaceae. Escherichia, Salmonella, and Bacillus species were the most prevalent species identified on the skin, gills, and intestines. Formulated feeds were more contaminated with bacteria than commercial feeds. The presence of the above microorganisms, some of which are pathogens (Salmonella enteritidis, Enterobacter aerogenes, Klebsiella oxytoca) to humans, is an indication that undercooked fish may pose health risks to susceptible human beings and an impediment to the rapid intensification of aquaculture as a result of mortality of fingerings.