Technical Abstract: Aspergillus flavus infects both plants and animals, and is of toxicological importance due to its production of aflatoxins (AFs) and other mycotoxins. Mycotoxins can cause agricultural losses totaling upwards of $1.4 billion annually. Recent efforts to reduce AF concentrations have focused on the use of the biocontrols AF36 and Afla-Guard, both of which contain nonaflatoxigenic A. flavus strains as an active ingredient. Biocontrols are applied to fields, where they competitively exclude native aflatoxigenic strains. Although biocontrol is effective, the extent to which these strains recombine with native strains, and the overall effect on fungal populations is unknown. Here, we show direct genetic evidence of sexual recombination between A. flavus strains, and that the recombination breakpoints in the F1 correlate to those inferred from population studies of natural isolates. Furthermore, we demonstrate that a crossover within the AF cluster can revert a nonsense mutation, resulting in a regained toxic phenotype. Finally we observed non-mendelian inheritance of AF cluster alleles in crosses with partial AF cluster parents. These findings indicate the possibility of cryptic heterokaryons in A. flavus that may be important in modulating AF production in stressful environments.