Red sea bream (Pagrus major) is an important aquaculture species in Japan. This study aimed to determine the ontogenetic development of the digestive system, enzyme activity and related gene expressions of red sea bream larvae from hatching to post-metamorphosis (40 days after hatching, DAH). The larvae were fed with the euryhaline rotifer Brachionus plicatilis species complex L-type enriched with Chlorella vulgaris containing DHA from 3 to 15 DAH followed by Artemia nauplii from 16 to 40 DAH. Post culture analysis included, histological analysis of the larval gut, enzyme assays (trypsin, chymotrypsin, lipase, pepsin) and real time PCR with larvae sampled from 1 to 40 DAH. At hatching, the larval digestive tract was undifferentiated and resembled a straight tube. There was low detection of enzyme activity and gene expression of trypsin, chymotrypsin, lipase, and amylase during yolk-sac stage, before mouth opened. At 3 DAH, the mouth opened and the larvae began to exogenous feeding followed by the differentiation of the digestive tract into buccopharyngeal capacity and intestine at 5 DAH. The pancreas, liver, and gallbladder were functional indicating the transition from endogenous to exogenous feeding. The enzyme activity and gene expression of trypsin, chymotrypsin, lipase, and amylase increased and fluctuated throughout the larval development, a pattern that is common among marine fish species. Pepsin activity and gene expression were not detected until 15 DAH and strongly increased from 20 DAH. Metamorphosis was complete by 40 DAH following the regular arranging of microvilli and the abundance of vacuoles in intestine.