© 2018 Elsevier B.V. The aim of this study was to describe the effect of the addition of commercial probiotics on the bacterial diversity in biofloc generated in a commercial farm of whiteleg shrimp Litopenaeus vannamei. The experiment consisted of a simple random design with three treatments by triplicate (two commercial probiotics: PA and PB, and one control, C). The PA was composed by a mixture (50:50) of Efinol PT and Mix Laboratory Robles; the second, coded as PB was composed by the mixture (50:50) of Epicin Ponds and Epicin Hatcheries. The control treatment, coded as C (natural endemic microbial consortium), consisted of the traditional biofloc system without probiotic application. The samples were obtained during tree periods of the shrimp nursery (beginning, medium and final). The abundance and diversity indexes (alpha, beta and gamma) were calculated. The shrimp productive parameters were determined. The ponds receiving the PA mixture registered 22 phyla, being Proteobacteria (49.99–53.66%), Planctomycetes (9.62–18%) and Bacteroidetes (11.41–29.66%) the most abundat. The ponds receiving the PB mixture, registered 19 phyla, and Proteobacteria (49.09–60.81%), Bacteroidetes (8.18–26.56%) and Planctomycetes (6.38–25.05%) were the most abundant. The control ponds had 19 phyla, and Proteobacteria (43.15–73.88%), Bacteroidetes (16.29–25.56%) and Planctomycetes (5.03–9.37%) registered the highest abundance. During the tree sampling periods, the Shannon index (alpha diversity) varied from 1.54–1.40 in PA; 1.34 to 1.41 in PB and 0.88 to 1.59 in C. The beta diversity indicated 86% of similarity among PA-C; and 90% among PB-C. At the end of the study, the gamma diversity in bioflocs depends 96% of alpha diversity and 3.70% of beta diversity. The autochthonous bacteria had the greatest influence on the diversity. The productive parameters did not show significant differences among treatments (P < 0.05).