More effective control of membrane biofouling in membrane bioreactors (MBRs) lies in the fundamental understanding of the pioneer microorganisms responsible for surface colonization that leads to biofilm formation. In this study, the composition of the planktonic and sessile microbial communities inhabiting four laboratory‐scale MBR systems were compared using amplified ribosomal DNA restriction analysis (ARDRA) and 16S ribosomal DNA gene sequencing. The ARDRA results suggest that the microbial communities on membrane surfaces could be very different from the ones in the suspended biomass. Phylogenetic analysis based on the 16S rRNA gene sequences provided a list of bacteria that might be the pioneers of surface colonization on microfiltration membranes. The results further suggested that research on the mechanisms of cell attachment in such an engineering environment could be critical for future development of appropriate biofouling control strategies.