From the conventional knowledge of protein nutrition to the molecular nutrition of amino acids, our understanding of protein/amino acid nutrition is rapidly increasing. Amino acids control cell growth and metabolism through two amino acid-sensing pathways, i.e. target of rapamycin complex 1 (TORC1) and the general control nonderepressible 2 (GCN2) signaling pathway. In the amino acid-abundant status, TORC1 dominates intracellular signaling and increases protein synthesis and cell growth. In contrast, amino acid deprivation actives GCN2 resulting in repression of general protein synthesis but facilitates the amino acid transport and synthesis process. By integrating and coordinating nutrition and hormone signaling, TORC1 and GCN2 control the switch of the catabolism and anabolism phase in most eukaryotes. Now, we appreciate that the availability of individual amino acids is sensed by intracellular sensors. These cutting-edge findings expand our knowledge of amino acid nutrition. Although the TORC1 and GCN2 were discovered decades ago, the study of molecular amino acid nutrition in aquaculture animals is still at its infancy. The aquaculture industry is highly dependent on the supply of fishmeal, which is the major protein source in aquacultural animal diets. Some concerted efforts were conducted to substitute for fishmeal due to limited supply of it. However, the concomitant issues including the unbalanced amino acid profile of alternative protein sources limited the utilization of those proteins. Continued study of the molecular nutrition of amino acid in aquaculture animals may be expected in the immediate future to expand our knowledge on the utilization of alternative protein sources.