Nutrition shapes the individual physiological pathways prior to hatching, resulting in long-term effects on postnatal growth and physiological functions. The environment, including nutrition, determines the rate of myogenesis, the number and size of muscle fibres, the composition of sub-cellular organelles, the patterns of gene expression, influences protein turnover and the efficiency of protein deposition, among others. Moreover, protein retention efficiency and fish adaptive fitness have been said to be negatively correlated. In addition, high mortalities are normally observed in the marine larval stages in optimized farming conditions (70–80%) affecting fish production. The consequences and implications of early nutrition for aquaculture production is an important challenge for the future. Likewise, optimized feeds need to be provided in sufficient quantities and in a manner adequate to feeding behaviour, to fully express growth potential, while avoiding deterioration of water quality or disease problems caused by excessive feeding. Understanding the mechanisms that control early development and growth and their relation with nutrition are critical for the identification of time windows in development that introduce growth variation, impact growth potential, and affect viability and quality of juveniles.