Commercial fishery processing results in discards up to 50% of the raw material, consisting of scales, shells, frames, backbones, viscera, head, liver, skin, belly flaps, dark muscle, roe, etc. Besides, fishing operations targeted at popular fish and shellfish species also result in landing of sizeable quantity of by-catch, which are not of commercial value because of their poor consumer appeal. Sensitivity to rapid putrefaction of fishery waste has serious adverse impact on the environment, which needs remedial measures. Secondary processing of the wastes has potential to generate a number of valuable by-products such as proteins, enzymes, carotenoids, fat, and minerals, besides addressing environmental hazards. Fishery wastes constitute good sources of enzymes such as proteases, lipases, chitinase, alkaline phosphatase, transglutaminase, hyaluronidase, acetyl glycosaminidase, among others. These enzymes can have diverse applications in the seafood industry, which encompass isolation and modification of proteins and marine oils, production of bioactive peptides, acceleration of traditional fermentation, peeling and deveining of shellfish, scaling of finfish, removal of membranes from fish roe, extraction of flavors, shelf life extension, texture modification, removal of off-odors, and for quality control either directly or as components of biosensors. Enzymes from fish and shellfish from cold habitats are particularly useful since they can function comparatively at lower temperatures thereby saving energy and protecting the food products. Potentials of these applications are briefly discussed.