The global demands for seafood products are steadily increasing and consequently numerous amounts of solid and liquid byproducts are generated that usually discarded leading to serious problems including loss of nutrients and environmental pollution that consequently negatively affect the human health. These byproducts are considered as an undiscovered treasure having the potentiality for the production of various probiotics as well as several biomaterials possessing multiple functional and biological activities. Nitrogenous compounds, lipids, polysaccharides and minerals are the main constitutive components that can be recovered or converted to value added products with potential nutritional, biomedical and pharmaceutical applications. Biological conversions via microbial fermentation and/or enzymatic treatment are eco-friendly economic processes that are widely applied leading to the production of bioactive protein hydrolysates, chitin based products and various industrial enzymes. In addition, algae based bioconversion is an efficient method for the valorization of seafood industry effluents via the production of various bio-refineries.