The present study was designed to assess the possible causes of the mass mortalities of Nile Tilapia Oreochromis niloticus at El-Behera Governorate, Egypt, in relationship to environmental and microbiotic factors. Water samples were collected from fish farms at different locations and from Lake Edku to analyze water temperature, water pH, salinity, biological oxygen demand, dissolved oxygen, total ammonia nitrogen, and un-ionized ammonia. A number of moribund and freshly dead fish were sampled and submitted to our laboratory for microbiological, molecular, and histopathological examination. Water analysis of the fish farms revealed noticeable increases in the previously mentioned physicochemical parameters. Clinical examinations of moribund fish showed severe gill rot and massive external and internal hemorrhages. Ordinary and molecular laboratory findings confirmed the presence of Branchiomyces sp. in gill tissue and mixed bacterial fish pathogens (Streptococcus agalactiae, Vibrio alginolyticus, V. parahaemolyticus, Pseudomonas anguilliseptica, and P. aeruginosa) in visceral organs. The histopathological and transmission electron microscopic examinations revealed severe necrosis of gill filaments and blockage of branchial blood vessels and lamellar capillaries with Branchiomyces sp. hyphae and spores mixed with different shapes of bacteria. Severe inflammations were detected in liver, kidney, heart, and brain tissues. Ultimately, we can conclude that the syndrome of mass fish kills in this area is a consequence of ecological damage to the aquatic environment, which is mainly related to natural and anthropogenic factors, as well as to the presence of infectious agents. Received September 30, 2015; accepted April 12, 2016.