Abstract: 【Objective】 To analyze whole genome sequence information of antagonistic bacteria Y4-39 against Phytophthora capsici, and to make clear its mechanism of antimicrobial and growth promotion, so as to provide a theoretical basis for its development and application.【Method】 The whole genome sequences of Y4-39 were determined using the thrid generation Oxford Nanopore Technology(ONT) and the second sequencing platform(BGISEQ). The whole genome of Bacillus velezensis Y4-39 with high inhibitory activity, isolated from intestinal tract of black soldier fly, was sequenced, and assembly, gene prediction and functional annotation were conducted for comparative genomics analysis. Then secondary metabolite synthetic gene clusters were identified and analyzed on the whole-genome level.【Result】 The whole genome of strain Y4-39 was 3891759 bp, with GC content of 46.67%, encoding 3713 genes, 27 rRNA, and 86 tRNA genes without plasmid. According to phylogenetic tree based on whole genome sequence, B. velezensis could be classified into 5 subgroups, with average nucleotide identity(ANI) between strains in the same subgroup greater than 97%, while ANI between subgroups above 98%. A total of 12 potential secondary metabolite synthetic gene clusters were predicted, including antimicrobial active substances such as surfactin, cyclic lipopeptide H, bacillaene, fengycin, difficidin, macrolactin and lichenysin, and 5 secondary metabolite synthesis gene clusters with unknown products.【Conclusion】 In B. velezensis, differentiation exists. Y4-39 genome sequence contains multiple secondary metabolite synthetic gene clusters, which is able to size antimicrobial active substances, thus boasting prospect of application.