A SBR was used in this study for investigating the influence of carbon source on EBPR metabolism and microorganism communities when feeding with acetate and propionate. The SBR was operated with a cycle time of 8 h and each cycle consisted of 4 min feeding, 2 h anaerobic period, 5 h aerobic period, 35 min setting, 15 min decanting and 6 min waiting. The COD of influent was kept at 300 mg/L during the experiment. Acetate and propionate were used as the sole carbon source for operation of 60 days, respectively. The phosphorus release/ COD consumption in the end of anaerobic phase were 0.35 and 0.27 when acetate and propionate were used as the carbon source, respectively. The PHA composition was different when different carbon source was dosed. PHB accounted for 92.6% in the end of anaerobic phase but the value for PHV was only 7.4% when acetate was selected as the carbon source. No PH2MV was detected during this process. The compositions of PHA were PHB (10.2%), PHV (35.8%) and PH2MV (54.0%) in the end of anaerobic cycle when propionate was used as the sole carbon source. There was variation of microorganism communities during this process for the results of DGGE combined with SEM micrographs and PHA staining. Coccus morphotype PAOs were accumulated in acetate-fed phase and rod morphotype PAOs were accumulated in propionate-fed stage. Different PAOs were accumulated and the metabolic pathways were different when different carbon sources were used, but good EBPR could be achieved during all these conditions.