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As aquatic food demand continues to increase globally and with the unexplored wild fish resources depleting rapidly expansion of aquaculture is needed to meet the demand. Genetic improvement breeding has come as an important tool that is aimed at increasing the efficiency and sustainability of aquaculture. Selective breeding, crossbreeding, hybridization, genetic engineering and other techniques are employed to increase the growth rate, disease resistance and adaptability to climate changes among other economically important traits. Although significant achievements have been made in some of the fish like the Atlantic salmon, tilapia and craps where these species are farmed to grow faster and improved disease resistance. Advanced molecular genetics like marker-assisted selection (MAS) and genomic selection have been employed in breeding programs that help more efficiently in trait selection. Genome editing technologies, specifically the CRISPR/Cas9 system, offer more innovative information. In addition, sustainability is another important factor to consider in the design of future breeding programs. Factors like nutrient pollution, habitat loss and genetic pollution from the domesticated strains escaping to the wild are some of the growing problems and also the lack of sufficient information on phenotypic and genotypic in many cultured species limited the potential use of breeding programs, indicating that data gathering and assessment must be done to increase progression. The chapter provides information on the techniques and technology used in aquaculture breeding. It also provides some insights regarding the challenges and environmental factors when such methods are involved.

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