As the number of native species targeted for aquaculture and enhancement in British Columbia (BC) rises, fisheries managers must develop policies and species-specific management plans that facilitate industry expansion while protecting the integrity and fitness of wild stocks. Whereas genetic introgression of domesticated stocks with wild stocks cannot be completely eliminated, some control can be gained by limiting the collection and culture of domesticated stocks to geographic units defined by the genetic structure of wild stocks. We describe the genetic structure of two species that are targeted for intensive enhancement and aquaculture in BC: Geoduck clams, Panopea abrupta and red sea urchins, Strongylocentrotus franciscanus. Based on a survey of eight polymorphic microsatellite loci, P. abrupta contained significant geographic structure within BC, with the distribution of genetic variation consistent with stepping stone gene flow under an isolation-by-distance model. A survey of seven polymorphic microsatellite loci covering a similar geographic range revealed genetic homogeneity of S. franciscanus in BC. Based on the different levels of structure displayed in the two species, we propose three geographically-based management units for P. abrupta and two for S. franciscanus in BC.