As the world’s food safety and environmental safety problems become increasingly severe, the agricultural sectors of various countries are also paying closer attention to the use of biofertilizers and biocontrol agents. Rhizosphere bacteria are a significant source of commonly used biofertilizers and biocontrol agents. This study aims to describe the genome and genomic traits of a biocontrol agent in the genus Bacillus. In this paper, a strain of Bacillus amyloliquefaciens IBFCBF-5 was isolated and identified to have an inhibitory effect on several common oomycete and fungal pathogens Phytophthora capsica, Sclerotinia sclerotiorum, Colletotrichum gloeosporioides, and Fusarium oxysporum f.sp. cucumerinum. The genome of strain IBFCB-5 was sequenced, and the assembled genome was 4,338,658 bp, with a G + C content of 46.05%. The IBFCBF-5 genome contains abundant GH, GT, CE, PL, AA, and CBM gene families, potentially degrading cellulose and hemicellulose, chitin, starch, xylan, peptidoglycan, etc. In addition, 14 lipopeptide and polypeptide antibiotic gene clusters were found in IBFCBF-5, including those coding for the synthesis of several known antifungal and antibacterial compounds Fengycin, Bacilysin, Bacillibactin, and Plantazolicin. Our results show that Bacillus amyloliquefaciens IBFCBF-5 has a broad-spectrum antifungal ability and that its genome contains many genes coding for enzymes involved in the synthesis of antimicrobial metabolites.