Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat.

Release of captively-bred individuals into the wild is one of the most popular tools in fisheries, forestry, and wildlife management, and introgression of hatchery-reared animals into wild populations is of global concern. However, research and monitoring of impacts on wild populations are generally lacking, and the benefit of hatcheries for long-term fisheries and conservation goals is unclear. Using spatio-temporal genetic monitoring and a four-dacade time series of catch data, we quantified the effects on the size and genetic diversity of wild populations of one of the world's largest marine stock enhancement programs-the red sea bream (Pagrus major) in Kagoshima Bay, Japan. Our analyses found that the stock enhancement program reduced genetic diversity of the population, but the genetic effect diminished with increased size of the wild population. Increases to the seaweed communities and reduced fishing efforts were the primary factors associated with the wild population recovery; effects of aquaculture were much smaller. Our results represent crucial evidence that hatcheries for enhancement and conservation of populations cannot be successful over the long term unless sufficient efforts are also made to reduce harvest rates and rehabilitate natural habitats.