The market of nutraceuticals and foods elaborated with natural additives are constantly growing and leading researchers and professionals of pharmaceutical and food industry to develop new products and reconsider the formulation of processed food. However, these products can only be insert into the market after extensive and well-performed scientific studies that clarify the mechanisms by which bioactive compounds can improve health status beyond nutrition or can replace conventional food additives perceived as “unhealthy” or “unfamiliar” by consumers. Therefore, scientific evidence regarding the actual health benefits and preservation/enhancement of food attributes are the crucial step in the exploration of nutraceuticals and natural food additives. In this context, several studies have been carried to identify and characterize natural bioactive compounds in aquaculture and related by-products for further production of nutraceuticals and food additives. The main purpose of this chapter is to highlight the most recent advances to explore extracts and isolated compounds from aquaculture and by-products to develop nutraceuticals and food additives.