In the present work，the structures and diversities of the microbial communities（bacteria and archaebacteria）in the water samples collected from the three-phase separator，the reaction tank，the filter and waterflood pump of the water treatment system in Baolige oilfield were studied through the high-throughput 16S rDNA sequencing technique when activating agents were added between the three-phase separator and reaction tank. In addition，the distribution and content of the oil recovery microbes in the four water samples were also analyzed. Results showed that the community structures of the bacteria and archaebacteria varied with the site of the water sample collected. The dominant bacterial groups in threephase separator，reaction tank，filter and waterflood pump were Campylobacteraceae，Tepidicella，Tepidicella，Azoarcus and Bacillus licheniformis，respectively. The dominant archaebacterial groups in the three-phase separator and the waterflood pump were both Methanomethylovorans. The diversity of the bacteria and archaebacteria in the water sample collected from the waterflood pump was lower than that in the previous site of sample collection，which indicates that the microbial community structure became simple compared with the previous water sample collection site. The concentration of the oil recovery microbes in the waterflood pump was the largest，which can be beneficial to the oil recovery when they are injected into the oil reservoir.