The study investigated the parasites affecting Oreochormis Niloticus (tilapia) from the Cagayan de Oro River. The study revealed that there were ten (10) species of parasites infecting the different organs of the fish samples, namely Protozoans: Oodinium pilluris (egg), Chilodonella sp., Coccidia sp.and,Cryptobia sp.; Nematodes: Capillaria sp., Procamallanus sp.,Spirocamallanus sp. and Camallanus sp.; Cestode: Hymenolypis nana; and Acanthocephala: Acanthocephalus sp. The skin, gills, and fins were the organs harboring most protozoan parasites. The internal parts most infected with the different parasites were the stomach and intestine of the fish. Two species of parasites, cestode and acanthocephalan, were found to harbor pigs as part of their life cycle. Among the three water sources, the highest incidence rate of infection with Protozoan, Nematode, Cestode, Acanthocephalan parasites was in Barangay Carmen. Aside from the piggeries put up along the riverbanks, Barangay Carmen also receives all the wastes coming from the upper parts of the Cagayan de Oro River, thus making the rate of infection high. Lowest incidence rate of infection with the parasites was in Barangay Consolacion. This is due to the salinity of the water. Most fish health problems occur because of environmental problems such as poor water quality and existence of parasites.