The main object of this study was to evaluate the effect of  two probiotic bacterial strains Bacillus sp. R2 and Planococcus sp. R11 and their mixture (1:1) on live food cultures (rotifers and Artemia) and study its effect on gilthead sea bream larvae until 40 day after hatching (DAH). Probiotics were supplemented  in the larval rearing system in triplicates in different strategies, which starting the exogenous feeding, by introducing to live food  through bio-encapsulation or in tank water or both. There was significance difference (P<0.05) in the survival and growth of S.aurata larvae that had probiotic achieved compared to control. Meanwhile total proteins, total lipids, fatty acid profiles were determined for live food during encapsulation and for the produced larvae after feeding. The results  showed increasingly significant difference (P<0.05) towards R11 probiotic treatments especially in bioencapsulation among all other treatments against control. Protease activity showed significant increase (P<0.05) in sea bream enriched with Planococcus sp. R11 led to the highest value (8.95 ± 0.21 U/mg) of enzyme activity in comparison to control (1.3±0.03 U/mg). Otherwise, the digestive system histology of larvae supplemented with bacteria in the period from  3-20 DAH showed improving number of goblet cells (37± 7.5), as well as number and length of villi (22±2.5and 35±9µm, respectively). Similarly,in the second duration from 20-40 DAH the number of goblet cells (96±14.4)was also increased, as well as the number and length of villi (27±2.5 and 126 ±25 µm, respectively(P<0.05)