Despite the expenditure of millions of dollars on restoration efforts for depleted North American stocks of alosine fishes, rangewide abundance levels for multiple species have declined to historic lows. Stocking practices aimed at rebuilding spawning runs are deemed successful when numerical abundance levels are shown to increase in response. However, these practices may only yield short-term gains in abundance at the ultimate expense of population genetic integrity and do not ensure the long-term persistence and evolutionary potential of a species. Although molecular methods are now widely employed in fisheries management and provide a suite of powerful management tools, these approaches have not been well integrated into alosine management strategies. We review the net effects of stocking practices on population genetic integrity and species' long-term persistence as it is currently understood and highlight what is known in this regard for alosines in North America, with particular focus on American shad Alosa sapidissima. We find that stocking practices carry a substantial risk to the persistence of genetically distinct alosine spawning populations and suggest that future restoration efforts proceed by providing access to historical spawning grounds, either through dam removal or through providing effective fish passage, followed by natural recolonization of reclaimed habitat. We also identify important areas of research relevant to future alosine restoration that require exploration and identify recent developments that may alter future restoration decisions in an adaptive management framework.