The pattern for distribution of genetic variation within and between populations is referred to as the genetic population structure of the species. To avoid depletion of genetic resources sustainable management should be based on knowledge of this structure. We discuss key aspects of genetic population structure in the context of identifying biological units for fisheries management, suggesting three basic types of structuring: distinct populations; continuous change; and no differentiation. The type of structure determines how units for genetically sustainable management are to be identified. We also review what is currently known regarding the genetic population structure of fishes exploited in the Swedish part of the Baltic Sea, and conclude that sufficient genetic information is lacking for most of the species. This is a serious problem, particularly considering that populations of several commercially exploited fishes are declining and some exhibit recruitment problems. For six species, Atlantic herring, Atlantic salmon, brown trout, European eel, turbot, and pike, sufficient genetic data are available to provide at least basic information on genetic structure and genetic units for biologically sustainable use. Current management practices do not sufficiently consider these data.