Patented, genetically engineered salmon are proposed for deployment in commercial aquaculture. If released accidentally into ecosystems, these novel organisms would have uncertain effects on ecological processes. Proponents suggest that ecosystems are fundamentally balanced and resilient and therefore that risks are negligible because of transgenic fishes’ reduced ecological fitness. Opponents maintain that ecosystems are characterized by instability and contingency rather than equilibrium and that a small number of ecologically fit organisms may change the state of an ecosystem if conditions are favorable. Current U.S. federal regulations hamper public discussion about potential risks, limit the role of agencies with the greatest expertise in fisheries and ecological sciences, and make precautionary action difficult without proof of harm. Field interviews and regulatory materials support the view that the U.S. regulatory system does not adequately address ecological and social issues, nor is current scientific knowledge sufficient for evaluation of potential risks to native ecosystems. Four elements are essential: independent scientific research before introduction that addresses uncertainties about potential impacts; regulatory systems with clearer standards and modified burdens of proof; opportunities for the public, including scientists, to participate meaningfully in decision processes; and for any introduction, experimental approaches that include hypothesis formulation, testing, and monitoring.