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Intensification of aquaculture production in Uganda is likely to result into disease out-breaks leading to economic losses to commercial fish farms and associated natural aquatic ecosystems. This survey assessed health profiles of selected commercial fish farms and adjacent natural aquatic ecosystemsto identify fish diseases and parasites affecting Nile tilapia (Oreochroms niloticus) and African catfish (Clarias gariepinus) in aquaculture systems in Uganda. Fish farms encounter disease out-breaks that cause low survival rates (0 - 30%), especially catfish hatcheries. Health management issues are not well understood by fish farmers, with some unable to detect diseased fish. Current control strategies to control aquatic pathogens include use of chemo- therapeutants and antibiotics. Bacterial pathogens isolated included Flavobacterium columnare, Aeromonas sp., Edwardsiella sp., Psuedomonus sp., Steptococcus sp., Staphylococcus sp., Proteus sp., and Vibrio sp. A high occurrence of Flavobacterium columnare exists in both asymptomatic and symptomatic fish was observed. Parasites included protozoans (Ichthyopthirius multiphilis, Trichodina sp. and Icthyobodo sp.) and trematodes (Cleidodiscus sp. and Gyrodactylus sp.). Diagnosis and control of diseases and parasites in aquaculture production systems requires adoption of a regional comprehensive biosecurity strategy: the East African (EAC) region unto which this study directly contributes.