Technical Abstract: Bacillus mojavensis, a specie recently distinguished from its previous Bacillus subtilis classification, was discovered in corn kernels and later determined to possess endophytic character. 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 30 B. mojavensis strains were subjected to genomic fingerprint analysis. A method was developed for differentiating the B. mojavensis strains from B. subtilis based on the diversilab automated microbial genotyping system, which involved analysis of rep-pcr amplified conserved bacillus DNA sequences. These experiments, when coupled with phenotypic analysis of the plant-bacteria interaction, will assist in the selection of B. mojavensis strains with the best biocontrol potential and provide further insight to the endophytic, and anti-fungal character of B. mojavensis.