Two Bacillus strains 373-2 and 411-1 showing good performance in zearalenone elimination, were screened from 400 strains of Bacillus. Zearalenone (15 μg/mL) could be eliminated completely after co-culture with the screened strains for 8 and 6 hours, respectively. Strain 373-2 and 411-1 were identified as a new species of Bacillus and Bacillus subtilis based on 16S rDNA sequence analysis. The mechanism of zearalenone elimination was also preliminarily investigated, and the result demonstrated that the main activity of zearalenone scavenging was due to the extracellular enzyme.