ABSTRACT: Previous studies of cod Gadus morhua population structure in European continental waters using molecular genetic markers have indicated high dispersal and limited structuring, in contrast to many tagging studies. More sensitive genetictechniques, in the form of microsatellite analysis, were used to reanalyse the population structure through the specific targeting of mature fish on spawning grounds. Significantly greater levels of differentiation were found than in previous studies,supporting the presence of 4 genetically distinct populations within the North Sea: Bergen Bank, Moray Firth, Flamborough Head and Southern Bight. Gene flow between the southern North Sea and eastern English Channel is largely restricted to populationswithin the Southern Bight (southern North Sea) and Beachy Head (eastern English Channel). The spawning stock in the central English Channel (Start Point) remains distinct from those in the Celtic Sea, Outer Hebrides, and central and northern North Sea. Noevidence of sub-structuring within the Irish and Celtic Seas was found, in contrast to previous genetic studies, although the populations remained divergent from that of the Outer Hebrides. All European populations were significantly divergent fromCanadian Scotian Shelf and Barents Sea (Bear Island) populations. The study indicates that the current fishery monitoring systems may need to be reassessed, particularly with respect to the North Sea, and highlights the value of using microsatellitescombined with the targeting of spawning stocks to investigate subtle population structuring.