The ethical issues raised by aquaculture were analyzed. A modification of the Ethical Matrix of the Food Ethics Council for the evaluation of novel foods was used; the Ethical Matrix was changed in order to include the various aquaculture production stages separately. The following stages were distinguished: the breeding stage, the growth/feeding stage, the “other-handling” stage (that includes disease and treatment, transportation of organisms, killing procedure, and DNA vaccinations), and the commercialization stage. The ethical issues concerning the producers, the consumers, the environment, and the aquacultured organisms, are discussed. This scheme was fitted to the intensive cage-culture of carnivorous fish. The differences with other forms of aquaculture are discussed, and how the scheme extrapolates to them. The ethical evaluation of aquaculture, in practice, will be rather a utilitarian balancing of cost and benefits of the respective actions. The desired characteristics of an ethical evaluation have been also outlined. Ethical evaluation should not be limited to a purely scientific analysis; it should be holistic, comparable to available alternatives, and should have the flexibility to incorporate new data generated in the fast growing/continuous changing aquaculture sector.