Bacterial communities in two full-scale wastewater treatment systems (system A and system B) with functional stability were monitored over 105 days using terminal restriction fragment length polymorphism (T-RFLP) based on 16S rRNA genes. During the study period, system A and system B were functionally stable. The effluent BOD concentration of two systems was always around 8 mg/L, and at the same time the effluent TN concentrations of two systems were always below 25 mg/L and 23 mg/L respectively. However, the T-RFLP profiles showed that for system A, the relative abundance of T-RF of 115, 118, 123, 471, 482 and 835 bp changed significantly. For system B, the T-RF of 123, 471, 750 and 835 bp changed significantly. The moving window analysis showed the average community change rates (every 15 days) of system A and system B were 21.5% +/- 5.7% and 22.6% +/- 5.0% respectively. Based on the Lorenz curves, it was observed for system A that 20% of the species corresponded with 43% to 50% of the cumulative relative abundance. For system B, 20% of the species corresponded with 47% to 52% of the cumulative relative abundance. In conclusion, the results of this study clearly revealed that, in the full-scale wastewater treatment systems, the functional stability did not correlate to the stable bacterial communities.