FS-3 and FS-7, Zearalenone (ZEN) degradation and acid tolerance strains, were isolated from grain and oil processing by-products and sewage sludge. FS-3 strain was identified as Bacillus Amyloliquefaciens and FS-7 strain was identified as Aspergillus niger. The bioactive substances of FS-3 strain could be secreted to medium, while FS-7 strain was intracellular. Under condition of pH 5, the degradation rates of FS-3 and FS-7 strains were 84.1% and 95.7%, respectively. Mass spectrometric for ZEN degradation products was performed and demonstrated that a new substance (M/Z=397) was appeared by FS-3 strain as well as two new substances (M/Z=213, 243) were appeared by FS-7 strain. The FS-3 and FS-7 strains were applied in the corn by-product fermentation process for ZEN detoxication, the result proved that ZEN content can be degraded from 4 345.8 μg/kg to 176.3 μg/kg and 431.83 μg/kg after fermentation for 3 days.