There are three general classes of threat to biodiversity at the gene level: 1) extinction, which result in complete and irreversible loss of genes; 2) hybridization, which may cause re-arrangement of co-adapted genes and loss of adaptability to local conditions, and 3) reduction of genetic variability within populations. While extinction avoidance is a fundamental management objective and hybridization can usually be dismissed in marine populations, the reduction of genetic variability within populations is a plausible threat and can occur in two ways. First, a decrease in population size may result in inbreeding. Normally, marine fish have very large population sizes, and commercial extinction is likely to occur long before populations are reduced to the level required for losses of genetic diversity due to inbreeding. However, when populations are very severely over-fished to small numbers, concerns associated with small population sizes and disruptions of migration between populations may become prominent. In particular, undetected populations within management units may be fished to this level before the situation is properly evaluated and remedied. Second, a reduction of genetic variability within populations may occur in a directed way, due to, e.g., selective fishing. Fishing is expected to generate selection on life history traits such as age and size at maturation; changes in life history traits influence the dynamics of fish populations, energy flows in the ecosystem, and ultimately, sustainable yield. We discuss management objectives designed to ameliorate genetic complications associated with small population size and fisheries-induced selection, and outline a management approach that may be useful when developing advice for maintaining genetic diversity.