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This Special Issue aims to collate recent and impactful studies that offer up-to-date insights and comprehensive research into the multifaceted roles of amino acids in aquaculture nutrition. From nutritional requirements to the functional roles of non-proteinogenic amino acids such as taurine, this Special Issue explores how amino acid supplementation influences stress response, immune function, antioxidant capacity, and overall health in fish and shrimp species. Altogether, the findings presented in this Special Issue highlight the potential of amino acids, not only as essential nutrients, but also as functional ingredients capable of enhancing performance, resilience, and robustness in aquaculture species. These insights will support the development of more effective and sustainable feeding strategies tailored to the physiological needs and health of farmed fish and shrimp.