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Challenging long‐held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod (Gadus morhua) is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km2 containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north‐east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank. [ABSTRACT FROM AUTHOR]

Fish stocks represent fundamental units in fisheries management, and their identification, especially in mixed-fisheries, represents one of the primary challenges to sustainable harvest. Here, we describe the first “real-time” genetic management program used to manage a mixed-stock fishery of a non-salmonid and commercially significant marine fish, the Atlantic cod ( Gadus morhua L). Based upon the analysis of >18 000 fish sampled from the commercial catch in Lofoten (Norway), which represents the largest remaining cod fishery in the Atlantic, we estimated the fraction of North East Arctic cod (NEAC), and Norwegian Coastal cod (NCC), just 24 h post-landing. These estimates, based upon the analysis of the Pantophysin gene, were performed weekly in the winter and spring of each year in the period 2007–2017. The program has successfully permitted the Norwegian Directorate of Fisheries to actively manage the commercial exploitation of the highly abundant NEAC stock, while simultaneously limiting exploitation of the fragile NCC stock, both of which overlap at the spawning grounds. Data from this program have also revealed a distinct temporal increase in the fraction of NEAC on the spawning grounds in this region, which is consistent with the overall increased abundance of this stock as estimated by ICES. [ABSTRACT FROM AUTHOR]