Abstract Although biofloc technology is already recognized as advantageous and practical for aquaculture for the effects of maintaining water quality and improving the health status and resistance of cultivated animals against pathogens, little is known about the way of action involved. This study aimed to evaluate the performance of bacterial groups as inducers in the formation of flocs compared to a system with spontaneous formation. Therefore, three microsystems were built in 3L tanks with constant aeration to induce the biofloc aggregation with addition of bacterial consortiuns with differentiated functions. It was used a control, without addition of bacterial consortium; B1 with addition of probiotic bacteria consortium; and B2, with adding nitrifying bacteria consortium. During the experimental period were evaluated physicochemical variables and quantifications of bacterial cultivable groups: Heterotrophic Bacteria and Vibrio. Also was the microscopic characterization of the flakes and tests of antimicrobial activity against pathogenic bacteria. Systems B1 and B2 showed promising results in relation to control (spontaneous bioflocs), showing more homogeneous flake formation, antimicrobial activity against the tested pathogens and greater biological diversity in the systems. The bacteria used in these tests were able to optimize the formation of microbial aggregates, showing potential for application in cultivation systems, in order to obtain improvements in productivity.