Global production of farmed fish and shrimp has grown dramatically over the past decades and now contributes to half of the aquatic products intended for human consumption. Aquaculture is a key sector for the maintenance and improvement of food security worldwide. However, its rapid growth has a significant impact on the environment, particularly on the stocks of wild fish used to produce aqua feed. In this context, aqua feed has dramatically evolved and has been adapted to many economic and environmental constraints. The use of fishmeal has particularly declined in favor of plant protein sources. But plant proteins are less adapted to the nutritional needs of fish and result in lower growth performances. Protein hydrolysates from fishing and aquaculture by-products are ingredients of high nutritional and bioactive potential developed to restore growth performances in high-level plant protein diets. They are rich in hydrolytic peptides and free amino acids, but they are complex mixtures whose composition is not well known. We developed an experimental approach to characterize the peptide fraction of two by-product hydrolysates based on two complementary approaches : a transcriptomics approach aimed at getting transcriptomics data about the targeted by-products, and a peptidomics approach. The peptidomics approach combined the optimization of fractionation steps and two complementary mass spectrometry techniques. Thus we identified more than 1,000 peptides in the two by-product hydrolysates. Furthermore, diet conditioning experiments conducted in sea bass, Dicentrarchus labrax, highlighted their interesting nutritional properties to maintain growth performances of farmed fish. Indeed, dietary inclusion of 5% of these hydrolysates in a high-level plant protein diet (95%) maintained growth performances at similar levels to those obtained with diets containing 80% of plant protein. In addition, we demonstrated an influence of these by-product hydrolysates on the digestive physiology of sea bass, as shown by biomarker expression in the intestinal absorption profiles observed in the study. Finally, our work shows that (i) both hydrolysates possess in vitro antibacterial activity and (ii) tilapia hydrolysate stimulates the immune system of sea bass. These results demonstrate the interest of using these two hydrolysates in aquaculture in addition to or instead of fishmeal.