The use of microorganisms of the genus Bacillus in aquaculture is a nutritional management practice that is rapidly expanding in regions with intensive fish farming. This study aimed to quantify the total bacteria and total coliforms from the intestinal microbiota and estimate the partial operating costs and growth performance of Nile tilapia (Oreochromis niloticus) of the GIFT strain. A total of 1,200 post-larvae (24.7 ± 0.50 mg) were distributed into 24 aquaria (0.03-m³ capacity) within a completely randomized design in 2 x 3 factorial (phase x bacteria), with four replications. Each aquarium, containing 50 post-larvae (sex reversal phase) or 30 fish (fingerlings phase), it was considered to be an experimental unit, consisting of three treatments (diet+Bacillus subtilis C-3102, diet+Bacillus cereus var. toyoi and diet without probiotic addition). The quantification of the total bacteria and total coliforms of the intestinal microbiota of tilapia were influenced (P < 0.05) by the stages of culture. The bacterial count was not influenced (P &gt; 0.05) by adding probiotics in the diets and no effect of the interaction between phase and bacteria was observed. The weight gain, average daily weight gain, specific growth rate and apparent feed conversion were not affected (P &gt; 0.05) by inclusion of probiotics as part of the diets. The inclusion of B. subtilis and B. cereus as part of diets for Nile tilapia promotes intestinal colonization and improves the survival rate without negatively influencing the feed intake, total biomass, gross revenue and partial operating costs and net revenue. Therefore it recommends the use of these probiotics to growth of tilapia fingerlings Nile, GIFT strain.