The effective application of genetic information in fisheries management strategies implies political goal setting taking both conservation and fisheries management into account. The concept of sustainable use as set out by the Convention on Biological Diversity offers a valuable starting point in this respect, since the criterion for it is defined as the maintenance of genetic diversity within each species. However, strategic decisions are also needed on the practical level, where the actual genetic information can be taken into account. Genetic factors, such as glacial differentiation, the postglacial genetic structure of populations, gene flow levels and the probability of the existence of adaptive differences, have an effect on the formation of conservation and management units and on the long-term strategy for the sustainable use of aspecies. The Atlantic salmon (Salmo salar) in the Baltic Sea area is treated here as an example of a complicated management problem with a highly hierarchical genetic structure associated with marked loss of naturally reproductive stocks, extensive hatchery production and an effective international offshore fishery. The implications of genetic factors for the conservation and management strategy of the Baltic salmon is discussed in the light of the goals set by the Convention on Biological Diversity, the Straddling Fish Stocks and Highly Migratory Fish Stocks Agreement, the Habitats Directive of the European Union and the International Baltic Sea Fishery Commission.