Objective <p>Domestication of fish for aquaculture involves the production of strains that differ genetically from their wild counterparts. This is a concern when commercial production occurs in installations from which individuals can escape into the wild and thereafter interbreed with wild conspecifics. Using a panel of 96 SNPs, we compared genetic diversity within and among samples of Atlantic halibut collected from aquaculture strains and from the wild across the species’ distribution range in the North Atlantic.</p> Results <p>All farmed samples differed significantly from the wild halibut samples and from each other. In contrast, no differences were found among the wild samples across the North Atlantic. Estimates of effective population size yielded low numbers (5.9 to 15.7) in all farmed strains, in contrast with infinite point estimates for all wild samples. The low estimates for farmed strains are consistent with extensive genetic drift as the primary cause of their divergence. We conclude that, because aquaculture-reared Atlantic halibut differ genetically from wild relatives, escapement of aquaculture-reared Atlantic halibut represents a potential threat to the genetic integrity of natural populations, should they interbreed in large numbers.</p>