The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation-by-distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the Eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation-by-distance signal along coastlines that mirrored previous microsatellite results, and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥ 84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coast samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation-by-distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low FST marine species.