Abstract: The treatment of flushing wastewater from scattered piggeries by anaerobic baffled reactor (ABR) was explored. The variations and differences of the microbial communities in the ABRs respectively with the influent mode-sequencing batch and the continuous operation under different pollution loads （3 operational phases) were compared. The results showed that, according to PCoA and cluster analysis, the microbial communities between the sequencing batch and continuous ABRs were similar under the same pollution load. The influence of the influent mode on microbial community structure was mainly presented in the first compartment (also the main removal area of COD). The five dominant genera in the continuous operation ABR were Clostridium_sensu_stricto_1, Norank_f_Anaerolineaceae, Christensenellaceae_R-7_group, Norank_c_Bacteroidetes_vadinHA17 and Norank_p_Candidate_division_WS6, with the relative abundance of 9.04%, 8.14%, 7.08%, 5.97% and 4.88%, respectively. While the five dominant genera in the sequencing batch ABR were Norank_c_Bacteroidetes_vadinHA17, Clostridium_sensu_stricto_1, Christensenellaceae_R-7_group, Norank_f_Anaerolineaceae and Desulfocapsa, with the relative abundance of 10.03%, 7.38%, 6.92%, 5.58% and 4.29%, respectively. Fisher’ exact test verified that there were 13 genera showing significant difference among the top 15 genera with high abundance in the two ABRs in the third stage, and the difference of 12 genera showed extremely difference (P≤0.001).