The identification of North Atlantic redfish has been controversial and remains a difficult task due to overlapping of meristic and morphological characters. Here we used nine microsatellite loci to assess the level of genetic differentiation among these species and assess the resolution power of these microsatellite loci for individual assignment-based analyses. Conventional analyses as well as individual Bayesian assignment methods clearly separated the four species of North Atlantic redfish as well as the giant form of Sebastes marinus and the so-called “oceanic” and “deep-sea” types of Sebastes mentella. Locus-by-locus analyses revealed that only five microsatellite loci out of nine used could discriminate the concerned species. The advantage of the Bayesian methods relies in the individual information retrieved. It therefore gave additional information on the interrelationship among species. Indeed, we provide evidence of potential hybridization among species as well as individual misclassification based on morphological identification. We provide a powerful tool to discriminate North Atlantic redfish species, which might be useful for legal issues such as poaching, unintentional harvesting and control label.