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The effects of a commercial probiotic (Clostridium butyricum) on growth, gut microbiota, digestion‐related enzyme activity, antioxidant capacity and water quality in genetically improved, farmed tilapia (GIFT; Oreochromis niloticus) were assessed in a closed‐circuit, container culture system. A basal diet containing commercially available C. butyricum at 3.0 × 1010, 1.5 × 1011 and 3.0 × 1011 CFU/kg, and a control diet were fed to tilapia fries for 90 days. Growth performances and water quality were improved by probiotic treatment. Activities of digestive enzymes (amylase, lipase and trypsin) were improved, especially with 1.5 × 1011 CFU/kg (p < 0.05). After feeding for 45 days and 90 days, antioxidant capacity in the liver, spleen and head kidney, and the plasma immunity in the treatment groups improved. The analysis of 16S rRNA indicated that C. butyricum did not significantly increase its abundance in the hindgut, but could modulate gut microbial communities and significantly increase functions relating to nitrogen metabolism, phosphorylation and proteinases. These results support the administration of C. butyricum, especially at 1.5 × 1011 CFU/kg. As a probiotic for high‐density tilapia, C. butyricum improves water quality, growth performance, antioxidant capacity and the immune response of GIFT under crowding stress. [ABSTRACT FROM AUTHOR]