Marine waste generated from industrial and commercial processing of popular species is an interesting source of bioactive and nutraceutical compounds. Moreover, mollusks such as squid, octopus, and bivalves, as well as other invertebrate species (jellyfish, cucumber sea, starfish, among others), are also promising but less explored sources for obtaining marine-derived bioactive compounds, namely bioactive peptides, polyunsaturated fatty acids complex saccharides, antioxidant molecules and pigments, among others. These bioactive molecules possess multiple applications in the health, food, and polymer industries. Several extraction and biotechnology processes have been developed to obtain this variety of compounds with biological activities, including fermentation and enzymatic maceration. This chapter explores the bioactive compounds in waste from little-studied but valuable marine sources and the biotechnology processes used for their extraction.