Digestive capacity varies substantially in marine fish larvae during development, and the formulation of larval diets does not take this into account. The objectives of this study were to assess in vitro protein digestibility of dietary ingredients throughout the ontogeny of digestive system in California halibut, Paralichthys californicus, larvae so as to identify adequate protein sources for each stage of development. Protein digestibility of potential sources was evaluated using the pH-STAT technique. Digestive enzymes utilized for the in vitro assays were obtained from homogenates of whole bodies (9, 15, and 26 days post hatch [dph]) and dissected guts of larvae (39 and 51 dph) sampled at different stages of development. Significant differences in degree of protein hydrolysis (DH) were found among developmental stages for some ingredients. Meals elaborated with rotifers and Artemia showed the highest DH with a tendency to decrease as larval development progressed. Digestibility of casein was poor early in development and increased as it progressed. In contrast, soybean and krill meals were poorly digested throughout development, which may be attributed to differences in the nature or quality of the ingredient. Results from this study highlight the importance of evaluating the digestibility of protein sources through larval development to formulate successful, stage-specific weaning diets.