Fomesafen, a broad-spectrum herbicide with a long duration, is frequently applied in legume farmlands, causing severe damage to crop growth and the local environment. Sinorhizobium sp. W16 was a fomesafen-degrading rhizobium isolated from a soybean nodule. The pure culture assay revealed that strain W16 efficiently degraded 5 mg L−1 of fomesafen by 69 % over 7 days. Three metabolites were identified by liquid chromatography and time-of-flight mass spectrometry, revealing strain W16 was the first strain isolated to catalyze the cleavage of ether bond of fomesafen. The results of the pot experiment demonstrated that strain W16 colonizes the soybean rhizosphere for over 50 days and eliminates the inhibition of fomesafen on nitrogen fixation by increasing the activity of nitrogenase and stimulating the indigenous nitrogen-fixing microbes in the rhizosphere. The symbiotic relationship between strain W16 and legumes promotes soil fomesafen degradation rates by 29.17 %–57.87 %. This study provides valuable information about a novel fomesafen-degrading rhizobium with great potential for promoting the bioremediation of herbicide-contaminated farmland soil due to the development of symbiotic systems with legumes.