Bacterial populations contaminating various tissues of fish cultured in fish ponds fertilized with different organic wastes have been studied. Twenty-five genera of bacteria were identified as associated with the fish tissues. The identified bacteria included one genus of spiral and curved bacteria, one genus of Gram-negative aerobic rod, sixteen genera of Gram-negative facultative anaerobic rods, one Gram-negative anaerobic bacterium, three Gram-positive cocci, two endospore-forming rods, and one Actinomycete. The bacterial contaminants were isolated from all tissues of the cultured fish. Higher bacterial contamination was associated with the gills, gut and skin than the blood and muscle. Although Pseudomonas sp. was most abundant species in the organic waste fertilized ponds and was present in considerable quantities in the five fish tissues, Salmonella sp. was the most important contaminant of the gills, muscle and skin. The presence of high diversity of bacteria in the fish tissues presents health hazards to both consumers and fish farm workers. Handling and cleaning of the fish can result in contamination of hands of farm workers and through them to their family members and others. The digestive tract and intraperitoneal fluid of fish in this study showed high concentrations of pathogens, such as Salmonella in fish cultured in the organic waste fertilized ponds, but lower concentrations in fish cultured in nonfertilized pond. Public health must therefore be of prime concern when dealing with fish farming and its products in countries, such as Ghana, with less restriction on release of waste into water bodies, and the use of untreated wastewater for aquaculture.