The present study aimed to detect the pepsinogen gene expression and pepsin enzyme activity, followed by ontogenetic development of gastrointestinal tube with emphasis on the functional stomach in Sobaity larvae (Sparidentex hasta) from hatching to 40 days post- hatching (DPH) reared at 21 °C. The exocrine pancreas including zymogens granules was detected coincident with the gradual yolk-sac absorption (1–3 DPH). The mouth and anus opened at 4 DPH simultaneously with the early convolution of the gut and its segmentation in anterior and posterior intestine, and the buccopharyngeal cavity. The most obvious differentiation in the digestive tract was the formation of an incipient stomach at 12 DPH, surrounded by striated muscle fibers and the development of the gastric glands. The functional stomach appeared 20 DPH onward, where it increased in size and the gastric folds elongated. The stomach was fully developed at 25 DPH with the transition from striated to smooth muscle cells and appearance of gastric glands in the posterior region of the stomach. Pepsinogen was not expressed before 12 DPH and significantly detected coincident with an increase in growth performance and also before the onset of weaning. It increased exponentially parallel to the larval stomach development and concomitant to the change in the diet from live to microbound food. The pepsin enzyme activity, even at a low level, was observed two days after pepsinogen gene expression (14 DPH), increasing sharply after the onset of weaning. Moreover, according to a phylogenetic tree based on the amino acid, the Sobaity’ sequence of pepsinogen was included in the subtype A2, when expressed during late larval development. These results enhanced our understanding of ontogenetic development of pepsinogen in this species, as the pepsinogen expressed earlier than when is expected, and suggest that farmers can initiate weaning at an earlier larval age than is currently practiced, regarding the fact that Sobaity larvae developed a functional stomach 25 DPH onwards.