Technical Abstract: Bacillus mojavensis was discovered in corn kernels and later determined to possess endophytic characteristics. The bacterium was also determined to have biocontrol potential due to its growth inhibition of the maize mycotoxic fungus Fusarium verticillioides. Maize plants with endophytic bacterium also displayed a marked improvement in growth and development, disease protection, and mycotoxin reduction. In an effort to further understand this relationship, and select suitable biocontrol candidates, a library of B. mojavensis strains was subjected to genomic fingerprint analysis. Subsequently, a phenotypic analysis of the strains was then compared to the genomic subtyping data to identify strains with beneficial endophytic properties. Furthermore the bacterial endophyte was transformed with the gene for the cyan fluorescent protein for endophytic colonization studies. These experiments formed the framework for developing methods of assessing fungal endophytic/bacterial endophyte/plant interaction for the use of B. mojavensis as an agent for the biocontrol of F. verticillioides.