The bacterial community on the surface of two polymeric membranes, polyvinylidene fluoride (PVDF) and polyethylene (PE), was investigated using fluorescence in situ hybridization. Three fouling states were defined during the study: low fouling (TMP10kPa), fouled (TMP20kPa), and extremely fouled (TMP40kPa), and the changes in the microbial communities on the membrane surfaces were monitored with the progress of fouling. Results showed that the polyethylene membranes exhibited a faster fouling tendency compared to the polyvinylidene fluoride membranes. Although the same microbial groups were found on the PVDF and PE membrane samples, their community dominance exhibited different trends with the advent of fouling.