The use of synthetic fungicides has caused major problems such as soil and water pollution and negatively affects non-target species. Microbial biocontrol agents are needed for crop disease management to reduce agrochemical use. Bacillus and related genera produce secondary metabolites with agricultural applications, such as the pathogen-control agent Bacillus velezensis. We isolated B. velezensis TSA32-1 from soil and identified its characteristics by sequencing its 16S rRNA. B. velezensis TSA32-1 showed enzyme activity and antimicrobial effects against phytopathogenic fungi by inhibiting the growth of Fusarium graminearum, F. fujikuroi, Alternatia alternate, and Diaporthe actinidiae. Additionally, B. velezensis TSA32-1 protected diseases in corn and pepper seeds caused by F. graminearum and Pythium ultimum. The complete genome of B. velezensis TSA32-1 was 4.05 Mb with a G+C content of 46.3 mol % and possessed the bacillaene biosynthesis cluster, a polyketide that inhibits protein biosynthesis. We also detected a surfactin synthesis cluster, known as non-ribosomal peptide synthetases, which biosynthesizes the antibacterial substance lipopeptide. Surfactin, and fengycin family compounds, secondary metabolites known as key factors in biological control, also detected B. velezensis TSA32-1 which shows potential as a biocontrol agent for controlling plant pathogens in agriculture.