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Potential management of the soilborne Aspergillus flavus and A. parasiticus fungi, a food contaminate that causes human and animal health problem, may be possible through maintaining an appropriate soil microbial diversity. The overall approach is to suppress aflatoxin producing fungi in soils through better understanding and manipulation of soil microbial populations. The objectives of investigation are 1) To develop bacterial profiles of selected soil samples from different rotational sequences: continuous peanut, continuous bahiagrass, peanut-cotton and peanut-corn; 2) To develop fungal community profiles of peanut soils and determine their relationship with A. flavus populations; and 3) To determine the effect of different cropping sequences on peanut aflatoxin contamination. The methodology included 1) determining the soil bacterial and fungal communities of different peanut cropping sequences utilizing a high resolution DNA fingerprinting technique, Automated Ribosomal Intergenic Spacer Analysis (ARISA); 2) 16S rRNA gene cloning and sequencing of bacteria populations from peanut soils; 3) the enumeration of A. flavus population levels and estimating the minimum detectable limits of these pathogens in soils; and 4) evaluating the aflatoxin content in peanut pod samples from different cropping sequences. The results indicated that cropping sequences and time of soil sampling have considerable effect on soil microbial community structure. Microbial diversity was higher in peanut soils with bahiagrass and cotton rotations over continuous peanuts. Rarefaction curves of 16S rRNA gene sequence data for all cropping sequences further showed bacterial diversity at species and genus level. The predominant bacterial divisions included Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes and Actinomycetes. The Proteobacteria populations have significant negative correlation with Firmicutes and are positively correlated with Gemmatimonadetes. The Actinomycetes division showed significant negative correlation with Verrucomicrobia. These relationships may indicate competition among bacterial species in agronomic soils. The minimum threshold limit at which A. flavus can be detected in peanut soils directly from soil genomic DNA with A. flavus specific primers was found to be 2.6 X 106 CFU g-1. Pod aflatoxin content was found to be less in pod samples when peanuts are rotated with bahiagrass and cotton over continuous peanuts. Our research results suggest these interactions between soil microbial communities in peanut soils may be manageable thus for suppressing peanut aflatoxin problem through different cropping sequences.