The interaction of nutrients, environment, and genome determines the general physiological functioning and health of an organism. The branch of science which aims to understand these interactions is known as "Nutrigenomics." Aquaculture and fisheries are the fast-growing food production systems and have an important role to play in achieving food and nutritional security. However, like other food production sectors, it also faces numerous challenges. Understanding the nutritional requirements and need-based dietary manipulation are perhaps the most effective and sustainable way of dealing with these challenges. In this review, we discuss the concept of nutrigenomics as a subset of multi-omics technology and highlight some studies encompassing nutrigenomics studies, with a specific focus on its application in fish nutrition. How these emerging techniques are applied in understanding various aspects of fish physiology as influenced by nutrition including nutritional supplements and various environmental factors like habitat, stress (temperature), and environmental contaminants have also been discussed.