The northern shrimp Pandalus borealis (ice. Stóri kampalampi) is a North Atlantic crustacean of significant commercial interest which has been harvested consistently in Icelandic waters since 1936. In Icelandic waters, the length at which this protandrous species transitions from male to female differs between the inshore and offshore populations, suggesting a biologically meaningful stratification which may or may not be plastic. Using reduced representative genomes assembled from RADseq data, sampled from 96 individuals collected at two time points (2018 and 2021), we compare the level of genetic structure across a gradient extending out of Skjálfandi bay, north Iceland. These data are compared to samples from a far offshore site, some 65 km out from the bay, as well as another inshore fjord in Arnarfjörður, in northwestern Iceland. Since 1999, no harvesting of inshore populations of P. borealis in Skjálfandi has been allowed due to stock decline, but harvesting of offshore stocks has continued. Uncertainty surrounding the extent of structure between the in- and offshore aggregations has remained. Here we report distinct genetic structure defining the inshore and offshore populations of northern shrimp, but find significant admixture between the two. Most importantly, we see that genetically inshore populations of northern shrimp extend far outside the harvest boundaries of inshore shrimp, and offshore individuals may exhibit punctuated migration into the inshore areas.