When raising fish for an aquaculture-assisted fisheries program, a key goal is to produce fish that are genetically similar to the wild stock. This is critical because a population’s genes determine its evolutionary fitness. There are two components of genetic management. The first, the topic of this chapter, is captive conservation genetic management which is needed to prevent random changes in gene and genotypic frequencies. The other component of genetic management is minimizing domestication, the topic of Chap. 3. Captive conservation genetic management is management of effective breeding number (Ne), which is the most important descriptor of a population; Ne is a population’s effective genetic size. Managing Ne is critical, because it is inversely related to inbreeding (changes in genotypic frequencies) and to genetic drift (changes in gene frequencies). These genetic changes are random, so inbreeding and genetic drift lower a population’s fitness (survival, growth, fecundity, etc.) in both the hatchery and the wild. Captive conservation genetic management is not a component of conservation aquaculture; management of Ne is needed to ensure that the fish that are raised in a conservation aquaculture program are not genetically depauperate, which will lower their post-augmentation fitness and the fitness of the wild stock following introgression. Recommended Nes needed to produce fish for aquaculture-assisted fisheries programs are presented. Various spawning protocols that can be used to maximize Ne are also presented.