The microbial community structures of a conventional activated sludge and MBR systems treating the municipal wastewater were studied using Fluorescent in-situ Hybridization (FISH) analysis to identify differences in both systems. The oligonucleotide probes specific for overall bacteria, including $alpha$-, $eta$-, and $gamma$-subclasses of Proteobacteria, ammonia-oxidizing bacteria (Nitrosomonas), and nitrite-oxidizing bacteria (Nitrobacter) were used to compare the microbial community structure of both systems. A trend of less hybridization with bacteria-specific probe EUB338 was observed in MBR systems operated under aerobic condition, compared to conventional activated sludge system. The less hybridization trend with the probes could be associated with low ribosomal RNA (rRNA) content in the biomass, which suggests that the biomass in the MBR system was not in a physiological state characteristic for growth due to low substrate per unit biomass.