Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. We characterized population structure and dispersal using neutral loci and loci putatively under selection and found evidence for a split into northern and southern population clusters. Further work on the putatively selected loci examined potential environmental drivers of adaptation among the sampled populations and identified minimum ocean temperatures as a potential selective force contributing to differentiation between clusters of scallop populations. This work not only helps refine the appropriate scale of management and conservation in this commercially valuable species, but also provides information that may be useful in improving the accuracy of future predictions and management strategies for the sea scallop.