Recognition of the limited biological resources and the increasing environmental pollution has emphasised the need for better utilisation of by-products from the fisheries. Currently, the seafood industry is dependent on the processing of the few selected fish and shellfish species that are highly popular with consumers but, from economic and nutritional points of view, it is essential to utilise the entire catch. In this review, we will focus on recent developments and innovations in the field of underutilised marine species and marine by-product upgrading and, more precisely, on two aspects of the bioconversion of wastes from marine organisms, i.e. extraction of enzymes and preparation of protein hydrolysates. We will deal with the question of accurate determination of fish species at the various steps of processing. Methods of genetic identification applicable to fresh fish samples and to derived products will be described.