Carotenoids and especially astaxanthin play a dominant role in the pigmentation of aquaculture species like salmonids and crustaceans. The color is an important quality criterion for consumers of fish and shrimp. This chapter reviews the targeted species for pigmentation and the use of astaxanthin in these species, the factors influencing pigmentation, the deposition of astaxanthin with some insights in its absorption, deposition and metabolism and its role in reproduction. The biological functions related to health, immunity and its antioxidant properties are described in aquaculture species as well potential benefits for humans. This chapter also includes an update on the safety and the regulatory aspects of astaxanthin for use in aquaculture species and its consumption as seafood by humans.