As interest and efforts in ecological restoration of native bivalve populations grow, the genetic implications of various restoration strategies are often unclear to resource managers and restoration practitioners, even though genetic considerations are vital to the ultimate success or failure of restoration endeavors. In an effort to fill this void, we present an overview of the underlying genetic concepts, a brief review of documented examples of native mollusc populations impacted by hatchery production, and a summary of the potential genetic impacts of restoration activities ranging from eliminating ongoing negative impacts with minimal genetic effects to intentional genetic manipulation of extant populations. We emphasize throughout the importance of understanding how adaptive, quantitative genetic variation is distributed within and among populations and the limitations of studies that address only selectively neutral molecular genetic variation. We also describe a conceptual framework for making genetically sound management and restoration decisions based on historical and current ecological and genetic considerations. Finally, because fully-informed decisions require a great deal of difficult-to-obtain data, we make suggestions on how to prioritize future research and outline practical measures that can be implemented in the absence of rigorous genetic data to prevent inadvertent negative genetic impacts by well-intended restoration efforts.