Abstract: To identify the dominant degrading 2,6-dinitrotoluene(2,6-DNT) and 4-mononitrotoluene(4-MNT) bacteria in the photocatalysis-anaerobic-aerobic progress, the microbe samples were collected individually from the inlet and outlet of 40 days running anaerobic-aerobic reactor. The measures of polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were cooperatively used to segregate microbes in the photocatalysis-anaerobic-aerobic microbial community for obtaining the dominant efficiently degrading 2,6-dinitrotoluene and 4-mononitrotoluene bacteria. It is found that the difference of microbe types is large at different locations in anaerobic reactor, but is less in aerobic reactor. There are five dominant microbes: Delta proteobacterium,Pseudomonas stutzeri, Pseudomonas trivialis,Burkholderia cenocepaciaand Chryseobacterium sp. AKB-2008-VA6 and one unknown microbes. The dominant microbes are facultative anaerobic-aerobic. The water quality is good in 40 days reactor operation.