Native shellfish aquaculture has many benefits, but interbreeding of hatchery and wild populations may pose genetic risks to wild populations. The type and magnitude of these risks depends in part on the genetic population structure of native shellfish species. Early genetic studies on marine shellfish provided little evidence for such structure. However, recent population genetic studies provide higher resolution, make use of both neutral and non-neutral molecular markers, and suggest some marine shellfish can exhibit population structure and even local adaptation. Here, we present preliminary results on genetic differentiation among populations of Crassadoma gigantea (the purple-hinged rock scallop) and Parastichopus californicus (the giant California sea cucumber), two native species that are currently being developed for aquaculture production in Puget Sound. Data for both species demonstrate high levels of genetic diversity and indications for population structuring by geography. Additionally, data for P. californicus suggest a potential cryptic species. Results will be used in a genetic risk model to quantify risk under multiple management scenarios, which will provide decision support to resource managers and other stakeholders. Our study shows the importance of population structure for genetic risk assessment and the power of combining empirical data, computer modeling and end-user input
