© 2019 Elsevier B.V. The aims of this study were to explore the effect of a probiotic consortium at different concentrations (low, medium and high) on bacterial community structure and composition in the hepatopancreas and digestive tract of Pacific white shrimp Litopenaeus vannamei reared under superintensive conditions, as well as to investigate its effect on gene expression of antioxidant enzymes. After the 69-day experimental period, shrimp treated with high probiotic concentration showed higher final growth, specific growth rate, weight gain and survival (p < .05) than those treated with low probiotic concentration or without probiotics; however, there were no significant differences compared to those treated with medium probiotic concentration. The analysis of the bacterial community structure revealed significant differences among treatments with and without probiotics; however, there were no differences between hepatopancreas and digestive tract samples, independently of the treatment received. Moreover, there were no differences in those samples from shrimp treated with probiotics at medium and high concentrations. The analysis of the bacterial community composition showed a higher proportion of Alphaproteobacteria (particularly members belonging to the family Rhodobacteraceae) in hepatopancreas and digestive tract samples from shrimp treated with probiotics at medium and high concentrations than in those treated with low probiotic concentration or without probiotics. In contrast, a higher proportion of Gammaproteobacteria (particularly members belonging to the families Alteromonadaceae, Moraxellaceae, Pseudomonadaceae and Vibrionaceae) was found in both sample types from shrimp treated without probiotics than in those treated with probiotics, independently of the concentration tested. At the end of the study, the levels of MnSOD (manganese superoxide dismutase) and CAT (catalase) transcripts were similar among hepatopancreas samples from shrimp treated with or without probiotics; however, the levels of GPx (glutathione peroxidase) transcripts drastically increased in those samples from shrimp treated without probiotics. These results could explain, in part, the mechanisms (i.e., competitive exclusion and immunomodulation) whereby probiotics confer beneficial effects to the host.