Abstract: Membrane bioreactor (MBR) is a new kind of technology in wastewater treatment and reuse. Because of the characteristics of long SRT and high sludge concentration in MBR compared with traditional active sludge process, the biomonitoring is a main parametric of the study of mechanism. The authors, combined with biological analysis methods, performed continuous monitoring on the microbiota in the sludge in MBR that was adopted to treat municipal sewage of laboratory test. It was found that the dominant microbiota population and number varied with the environment and changed in certain rule. The dominant population was alternate and in some order: running ciliated protozoa, tubifex, ciliated protozoa, rotifers and vorticella, then arcella. After filamentous bacterium bulking the number of microbiota decreased, and rotifers, epistylis and arcella became the main population. The microbiota ate sludge to limit the sludge content, and on the contrary the sludge controlled the microbiota either. In a word, the microbiota and active sludge affected each other, and in a dynamic balance.