Based on fomesafen residue toxicity in soil, the strain FB5, which can utilize fomesafen as the sole carbon source, was isolated from a fomesafen-contaminated soybean field in Heilongjiang province, China. It was found to degrade 88.32% of 500mg/L fomesafen within 96h. Conbined with morphological, physiological, biochemical characteristics and 16S rDNA sequence, the strain was identified as Shigella flexneri. After evaluating the effects of environmental factors such as temperature, fomesafen concentration, and primary pH, the optimum growth conditions of the strain were obtained. A remarkable remediation ability of the strain to fomesafen–polluted soils was demonstrated by a sensitive crop bioassay in pot soil. This will provide a new suitable candidate for fomesafen biodegradation and a workable pathway for solving the hazards of fomesafen residues in agricultural soils.