In this study, we have evaluated the incorporation of two types of protein hydrolysates at 9 and 12% levels of inclusion, one from yeast (Saccharomyces cerevisiae, YPH) and another one from pig blood (PBPH), in microdiets for gilthead sea bream (Sparus aurata) larvae, and compared these results to a microdiet containing fish protein hydrolysate and another group only fed with enriched live prey (rotifers and Artemia). The trial consisted in substituting up to 75% (wt/wt) the enriched Artemia with the experimental microdiets from 15 to 40 days post-hatch, whereas larvae were exclusively fed on microdiets from 40 to 55 dph. Protein hydrolysates used in the present study were obtained from different raw materials (yeast, pig blood and fish protein concentrate) and differed in their amino acid (AA) profile and in their molecular weight distribution. YPH and PBPH were mainly composed by free amino acids (FAA) (44%, MW < 200 Da), di- and tripeptides (50%, 200 < MW < 500 Da) and 6% of larger polypeptides (500 < MW < 2500 Da); whereas the fish protein hydrolysate (FPH) did only contain a minor quantity of FAA (1.5%) and was mainly composed of di- and tripeptides (36.5%) and larger polypeptides (51.4%, 500 < MW < 2500 Da). The contents in FAA and di- and tripeptides in the microdiet containing FPH were 0.2 and 4.4%, respectively. FAA levels in microdiets including YPH and PBPH at 9 and 12% were 4.0 and 5.3%, whereas levels of di- and tripeptides were 4.5 and 6.0%, respectively. Results revealed that FPH in microdiets for marine fish larvae may be replaced by alternative protein hydrolysates obtained from yeast and pig blood, as fish fed with those diets performed, in terms of growth, survival, level of maturation of the enterocytes (activity of cytosolic and brush border enzymes) and incidence of skeletal deformities, as well as those larvae fed with only enriched live preys (rotifers and Artemia). Using YPH and PBPH, the inclusion level of protein hydrolysate in microdiets might be reduced to 9% (3% lesser to actual practices using fish protein hydrolysates) without affecting larval performance. Present results suggested the importance of leucine, valine and phenylalanine in fish larval skeletogenesis and in the appearance of skeletal disorders.