Abstract: To clarify the proteomics mechanism of fomesafen degrading bacteria. Focusing on the highly efficient degrading bacterium Shigella flexneri FB5 screened and obtained in lab, and based on the efficient degradation of fomesafen in this strain, protein extraction and two-dimensional electrophoresis were carried out. 13 paraproteins appeared among the strain induced by fomesafen were found, and they were identified by mass spectrometry. The function was gained by bioinformatics alignment, and PCR amplification and sequencing were conducted on the target protein genes. The results showed that the two related genes of strain induced by fomesafen were obtained. After sequencing, it was found that the homology between the gene F3 sequence and the dps gene of E.coli- binding protein was 100% . The similarity of gene F6 sequence, salmonella enteric subtype serotype S1635 outer membrane protein gene and E.coli SYW004 external membrane protein gene A was 87%, at the same time the function of these gene-families was analyzed, the physicochemical properties were speculated.