Résumé : Biofouling significantly reduces the performance efficiency of membrane bioreactors due to the colonization and accumulation of a matrix of microorganisms. In order to investigate the effect of ultrasonic frequency on biofilm formation and bacterial ecology at different frequencies, four microfiltration membrane modules were subjected at 0, 20, 30 and 40 kHz in pilot-scales. The results of massive parallel sequencing showed that the application of ultrasonic frequency significantly affected the bacterial population in biofouling and modifies the species richness even at low frequency. This research reveals that the application of ultrasonic frequencies avoids the colonization of Acinetobacter genus, which is considered an initial colonizer of biofouling and clogging in the submerged membrane reactor, fact that caused problems in full-scale wastewater treatment plant. The promotion of Gordonia genus was observed during the application of any ultrasounds frequencies (20,30 and 40 Hz). The compositional statistics data exposed the similarity of bacterial communities under medium-high ultrasonic frequency, while those great distances were found in both low and no-ultrasounds frequencies apply. These results suggest that the application of ultrasounds in membrane bioreactor for treating wastewater could be effective in the potential reduction of biofouling formation in order to improve the to improve the useful life of this system with short periods of application of ultrasound.