The genomes of the three strains of Aspergillus flavus with demonstrated utility for the biological control of aflatoxin were sequenced. These sequences were assembled with MIRA and annotated with Augustus using A. flavus strain 3357 (NCBI EQ963472) as reference. Each strain had a genome of 36.6 MB, a G+C content of 48.3% and had approximately 11 thousand genes mapped to strain 3357. This whole genome sequence is valuable for basic biological, agricultural, and epidemiological research by facilitating the identification of specific strains.