Abstract Although many aspects of aquaculture have changed very dramatically over the last 50 years, one feature that has not changed very much is the use of natural genetic resources as the primary supply of 'raw material' for use in production facilities. Consequently, some serious attention should be paid to the factors that affect natural aquatic genetic resources and their conservation. Three major factors are identified that can have a major impact on the natural genetic resources in the marine environment: habitat alteration, changes in the commercial fishery, and use of aquaculture to restore or enhance natural populations. The genetic effects of each of these factors are discussed. With this diversity in potential effectors, there is some 'genetic risk' associated with introducing an additional component to the natural system, e.g. intensive aquaculture systems. Minimization of genetic risk can be accomplished by maintaining genetic variability within natural populations and a model is discussed to evaluate the characteristics of an aquaculture species that can be utilized to minimize loss. Only through understanding how major genetic alterations are introduced, what their impacts are, and how these are addressed can a marine aquaculture operation be managed in a viable and sustainable manner.

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