Field plot studies indicate that both the environment and cotton production influence the magnitude and composition of Aspergillus flavus group fungi. The magnitude of A. flavus group populations associated with cotton crops fluctuates broadly both during the year and between years. These fluctuations provide opportunities to incite rapid changes in population composition through the application of organic matter colonized by specific strains A. flavus early in the cotton season. In this manner, application of atoxigenic strains of A. flavus has been shown to provide an avenue for managing aflatoxin contamination. These strains compete with and displace toxigenic strains and reduce the ability of A. flavus populations to produce aflatoxins. There is variability among A. flavus strains in a variety of traits and our observations on the distribution of atoxigenic vegetative compatibility groups suggests certain A. flavus strains are adapted to particular growing areas. Thus, it may be necessary to utilize atoxigenic A. flavus strains adapted to regional conditions in order to effect long term changes in A. flavus populations.