The rapid development of aquaculture production throughout the world over the past few decades has led to the emergence of new scientific chal lenges to improve fish nutrition. The diet formulations used for farmed fish have been largely modified in the past few years. However, bottlenecks still exist in being able to suppress totally marine resources (fish meal and fish oil) in diets without negatively affecting growth performance and flesh quality. A better understanding of fish metabolism and its regulation by nutrients is thus mandatory. In this review, we discuss four fields of research that are highly important for improving fish nutrition in the future: ( a ) fish genome complexity and subsequent consequences for metabolism, ( b )) microRNAs (miRNAs) as new actors in regulation of fish metabolism, ( c ) the role of autophagy in regulation of fish metabolism, and ( d ) the nutritional programming of metabolism linked to the early life of fish.