The collapse of marine fisheries worldwide has forced recognition of the fact that sustainable fisheries management cannot be achieved without a reasonable understanding of stock structure. Fisheries focusing on species that exhibit seasonal migrations between spawning and feeding grounds should consider the composition of feeding aggregations of presumed mixed origin. Using nine microsatellites and the Pan I locus, we assess the contribution of two previously described major spawning components of Icelandic cod Gadus morhua (southwest and northeast) to two large feeding and two large juvenile aggregations of presumed mixed origin and situated in the northwest and northeast of Iceland. The Bayesian approaches (STRUCTURE and BAYES) revealed that, with the exception of the juvenile samples collected in 2002 and 2003 in the northeast, most of the individuals originated from the southwest. These results confirmed that the Icelandic cod exhibit a complex biological pattern involving spawning site fidelity and migration to and from feeding aggregations. The sustainable management of the Icelandic cod is likely to be compromised if its complex dynamics is not properly integrated into fisheries management plans.