Fish protein hydrolysates used in larval diets have been prepared from a variety of fish species, with different enzymes used to hydrolyze the protein. This study's objectives were to determine the effect of the dietary inclusion of fish muscle hydrolysates obtained from species-specific muscle/enzymes-versus hydrolysates produced from muscle/enzymes of a different species-on the growth performance, survival, skeletal development, intestinal peptide uptake, and muscle-free amino acid (FAA) composition of larval Walleye (Sander vitreus). Eight protein products were obtained for this study, comprising an unhydrolyzed and hydrolyzed product from each combination of muscle/enzymes from Walleye and Nile tilapia (Oreochromis niloticus). Four diets were produced, and the dietary protein was provided in a 50/50 ratio of unhydrolyzed and hydrolyzed protein from the respective muscle/enzyme combination. Four groups were fed one of the corresponding formulated diets, and two groups of larvae, fed a commercial starter diet and Artemia, respectively, served as reference groups. Larval Walleye fed the diet containing protein produced with the species-specific muscle and enzymes had a significantly higher weight after the study-30% higher than any other group. A significant interaction effect between muscle and enzyme sources on the growth of Walleye larvae was observed. The species-specific combination also led to a significant increase in postprandial FAA and indispensable amino acid concentrations in muscle. No significant differences were observed between the hydrolysate-fed groups in survival, deformity occurrence, or peptide uptake. Each hydrolysate-based diet significantly reduced skeletal deformities and survival compared to the commercial diet. The results of this study suggest that species-specific muscles and enzymes produce a more optimal dietary protein source for larval fish than non-species-specific products. Further research should focus on improving the physical properties of the formulated diets to reduce possible leaching of hydrolyzed protein and improve the survival of fish larvae.