Abstract Numerous leaders in fisheries science highlight the need for improved governance of our oceans, especially in relation to Unreported and Unregulated Fishing (IUU) activities. The global impact of the ongoing and relentless loss of fish biomass, biodiversity and fisheries income adds, not only considerable uncertainty to our forecasts of sustainability, but also there are concomitant threats to ecosystem function, food security and the economic and social viability of fishing communities. In this context, population proteomics is becoming a powerful tool enabling the study of the population structures and functional adaptations to environment from human settlement to animal natural populations. A proteome scan approach based on two-dimensional fluorescence difference gel electrophoresis (DIGE) technology has been applied to generated thousands of protein markers that allow the identification of different hake (Merluccius merluccius) population, a species of most important interest to fisheries and human consumption. Based on quantitative differential analysis of hake populations, several protein markers were selected that reliably assigned individuals to the populations of origin. These new methods have the potential to complement, and in some cases, even supplement more established approaches, as they rapidly respond to the environment where the fish was living just prior to capture, and therefore provide information on geographic origin, etc.