Metabolic mechanisms underlying the divergent response of rainbow trout (Oncorhynchus mykiss) and Nile tilapia (Oreochromis niloticus) to changes in dietary macronutrient composition were assessed. Fish were fed one of four isoenergetic diets having a digestible protein-to-digestible energy (DP:DE) ratio above or below the optimal DP:DE ratio for both species. At each DP:DE ratio, fat was substituted by an isoenergetic amount of digestible starch as the non-protein energy source (NPE). Dietary DP:DE ratio did not affect growth and only slightly lowered protein gains in tilapia. In rainbow trout fed diets with low DP:DE ratios, particularly with starch as the major NPE source, growth and protein utilisation were highly reduced, underlining the importance of NPE source in this species. We also observed species-specific responses of enzymes involved in amino acid catabolism, lipogenesis and gluconeogenesis to dietary factors. Amino acid transdeamination enzyme activities were reduced by a low dietary DP:DE ratio in both species and in tilapia also by the substitution of fat by starch as the NPE source. Such decreased amino acid catabolism at high starch intakes, however, did not lead to improved protein retention. Our data further suggest that a combination of increased lipogenic and decreased gluconeogenic enzyme activities accounts for the better use of carbohydrates and to the improved glycaemia control in tilapia compared with rainbow tront fed starch-enriched diets with low DP:DE ratio.