In connection with the increasing population in the world, the food industry has been developing rapidly and the industrial by-products have become an important problem. Fish industry byproducts are rich in minerals, nitrogen, and fat, and can contribute to environmental pollution if not properly treated. These byproducts are generally evaluated for biogas production and/or follow wastewater treatment. The byproducts can alternatively be utilized for the cultivation of microorganisms and converted to value-added products. For this purpose, two edible filamentous fungi, namely Aspergillus oryzae and Rhizopus oryzae were used to evaluate the production of protein-rich fungal biomass from fish processing byproducts. The amount of fungal biomass and its protein content (35-65%) varied according to the origin of the byproduct within the fish filleting process. Along with the fungal growth and production of a protein-rich product, nitrogen and COD removal of 32–72% and 12–58%, respectively, were achieved. Altogether, cultivation of filamentous fungi can aid to divert fish processing byproducts from biogas production towards production of protein-rich products for animal feed and concomitantly ease wastewater treatment.