Microorganisms isolated from the super-intensive marine shrimp system with microbial bioflakes (Bacillus spp.) were cultivated in 100 mL flasks with sterile bacteriological BHI broth for 24 h at 30 °C in a bacterial incubator. Subsequently, microorganisms were separated from the culture media by centrifugation at 4000 ×g for 30 min at 4 °C. The precipitate was resuspended in sterile saline water with 3% NaCl (Synth®, Diadema, SP) and the concentration was adjusted to 104 CFU·mL− 1 with previously constructed standard curve (OD 630 nm). After preparation of the solutions, they were added at a concentration of 104 CFU·mL− 1 in post-larval culture tanks. The microbiological parameters of the culture water in bioflakes were analyzed. Therefore, 10 mL samples of water from each treatment were collected every five days of the experiment, using 15 mL sterile test tubes with screw caps for determining the microbial count in the water (counting viable heterotrophic bacteria and Vibrionaceae). However, 1 mL samples were inoculated in serial dilutions through saline tubes (3% NaCl) and 100 μL of the samples was seeded on Petri plates containing bacteriological culture medium and Marine Agar and Thiosulphate Citrate Bile Sucrose (TCBS) Agar for counting viable heterotrophic bacteria and Vibrionaceae, respectively. Later, they were incubated in a bacterial incubator at 30 °C for 24 h and counted the next day using the method of counting plates on colony forming units (CFU·mL− 1).