Strain MS455 is an endophytic bacterium isolated from a soybean plant growing in a charcoal rot disease patch in Mississippi. It possesses a broad-spectrum antimicrobial activity against plant pathogenic bacteria and fungi including the charcoal rot disease pathogen Macrophomina phaseolina. The bacterial strain was preliminarily identified to be member of Burkholderia pyrrocinia. Random mutagenesis revealed that a nonribosomal peptide synthetase gene is required for MS455 antifungal activity. The complete genome of strain MS455 was obtained by PacBio sequencing. Genomic analysis revealed that the MS455 genome consists of three chromosomes and one plasmid. The gene targeted by transposon in a mutant was localized in a 57-kb gene cluster which consists of fifteen open reading frames (ORFs). ORF15, located at the right border of the gene cluster, was predicted to encode a LuxR-type transcriptional regulator that is associated with regulation of production of antifungal activity. Site-specific mutagenesis and complementation of the ORF15 gene are under way to characterize its function in antifungal activity. This research will provide critical clues for development of biologically-based approaches for plant disease management.