Silkworm excrement is the main organic waste in silkworm production, and it is rich in nutrients and microbial flora. Bacillus subtilis SEM-2 Strain was isolated from the silkworm excrement. The study showed that the isolate has good effects on antagonizing Fusarium. For further analysis the relevant mechanism, genome sequence of these isolates were sequenced using Illumina HiSeq 4000 sequencing platform.