Abstract: 【Objective】 To analyze whole genome information of Bacillus velezensis MC2-1, and to discover genes related to antagonistic substance synthesis in this strain, so as to provide data for biocontrol mechanism research and application.【Method】 Whole genome of antagonistic bacterium MC2-1 isolated from intestinal tract of Periplaneta americana against Phytophthora nicotianae was sequenced using Illumina HiseqII platform and PacbioIII platform, and genome assembly, gene prediction, functional annotation, synteny analysis and prediction of secondary metabolite synthetic gene clusters were conducted.【Result】 The whole genome was 3929792 bp with average GC content of 46.5%, which encoded 4015 genes;and the genome of MC2-1 strain had 86 tRNA, 27 rRNA, 81 sRNA;2 genomic islands, 1 prophage and 9 CRISPR-Cas. In NR, Swiss-Prot, COG, GO and KEGG databases, 4015, 3347, 2996, 2841 and 2223 potential genes were annotated. At the same time, related enzyme genes such as chitinase, cellulase and amylase that could degrade cell wall of phytopathogenic fungi were annotated in the CAZyme database. In addition, 12 secondary metabolite synthesis gene clusters were predicted in MC2-1, encoding inhibitors such as Surfactin, Fengycin, Bacillibactin, Baclysin, Macrolactin H, Bacillaene and Difficidin, most of which were synthesized through non-ribosomal pathway and polyketide synthase pathway and 6 of these gene clusters were highly conserved in B. velezensis.【Conclusion】 Strain MC2-1 genome contains a variety of secondary metabolite-encoding gene clusters, which can encode and synthesize existing antimicrobial substances and genes that can degrade cell wall of phytopathogenic fungi. Therefore, it is predicted that strain MC2-1 can secrete secondary metabolite and enzymes to prevent and control plant disease, enjoying prospect of application in agricultural biocontrol.