Fishmeal substitution with sustainable feed sources is highly essential towards sustainable production. This study aimed to investigate the effects of substituting fishmeal (FM) with Daphnia magna biomass meal (DBM) or zooplankton biomass meal (ZBM) on growth performance, liver and intestinal histology, gut bacterial abundance and stress tolerance of Nile tilapia, Oreochromis niloticus, fry. Nile tilapia fry (0.23 ± 0.04 g) were randomly assigned to five groups of three replicates. The control diet comprised 300 g/kg FM, and the FM was substituted with DBM or ZBM at levels of 25% and 50% (DBM‐25, DBM‐50, ZBM‐25 and ZBM‐50 respectively) in the other experimental diets. The experiment lasted 56 days in 1.5 m3 concrete tanks. The results revealed that weight gain and feed conversion ratio (FCR) significantly (p ≤ 0.035 and 0.025 respectively) improved with a polynomial response with a peak at 25% ZBM and a linear increase with DBM up to 50% of FM. Histometric indices of the distal intestine showed improvements (p ≤ 0.001) in villus height, villus width, crypt depth and muscle thickness of fish fed DBM or ZBM compared to the control. In the meantime, there were no histological abnormalities in the liver sections. The replacement of FM with DBM or ZBM could modulated gut bacterial abundance, including total bacterial count, Escherichia coli, Bacillus subtilisand Lactobacillus sp. The fish‐fed DBM or ZBM‐containing diets had higher (p ≤ 0.05) tolerances to salinity stress than the control group. In conclusion, DBM or ZBM could replace FM up to 50% and 25%, respectively with improved fish growth performance, FCR, gut histology and tolerance to salinity stress. K E Y W O R D S Daphnia magna, growth, intestinal bacterial abundance, salinity stress, zooplankton Oreochromis niloticus