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Anecdotal and empirical evidence exists for substantial (up to 40%) declines in growth among Oreochromis populations domesticated in both large and small‐scale fish farms in Africa. These declines are at least partly attributable to poor genetic management, including inadvertent selection, inbreeding, bottle‐necks and founder effects. Due to restricted cash flow and investment capital, genetic management and selective breeding for the improvement of domesticate populations are difficult for small‐scale farmers, but feasible on larger‐scale farms. In managing domesticated gene pools, feral populations can serve as a broodstock reservoir, making the use of indigenous species advantageous. A development model of large‐scale hatcheries producing selected lines of sex‐reversed, indigenous tilapia for sale to smaller‐scale farmers is proposed as a solution to the problems of poor genetic management in African aquaculture.