Abstract The rising demand for seafood and trade globalization has brought about a rapid increase in the number of fish species traded. Consequently, the occurrence of mislabelling is growing as well, reaching levels of concerns in USA, Canada and Europe. In this light, the evolving consciousness of consumers and the new exigencies of commerce call for greater safety and quality requirements. These factors have made urgent the need for efficient traceability systems, aimed to ensure transparency on the identity and origin of the traded products and the compliance with the regulations concerning illegal fisheries and labelling. Moreover, greater efforts are necessary to create a list of market names that can be recognized both locally and internationally, in order to overcome the confusion regarding fish denominations. In this context, molecular analysis represents the most promising challenge to verify and support traceability in the seafood chain. Nowadays, the three mitochondrial genes cytb , COI and 16srRNA are the most targeted for this purpose and, among the available procedures, the DNA bar coding is the most commonly applied to verify the labelling compliances, also at the official level. In this review, the most important issues relating to these topics have been reported and discussed.