Technical Abstract: Aflatoxins are toxic polyketides produced by several Aspergillus species that contaminate food crops worldwide. Aspergillus flavus and A. parasiticus are the most common agents of aflatoxin contamination of oil-rich crops. The genes involved in aflatoxin biosynthesis are clustered and convert acetate and malonate to aflatoxins B1, B2, G1, and G2. We determined the frequency of the MAT1-1 and MAT1-2 mating-type genes in A. parasiticus and A. flavus sampled from single peanut fields in the United States (Georgia), Africa (Benin), Argentina, Australia, and India. Population samples for each species were clone corrected using multilocus sequence typing, which included two aflatoxin cluster regions (hypE and aflW/aflX), three non-cluster genes (trpC, amdS and a hypothetical protein encoding gene), and the MAT gene. Analysis of molecular sequence variation across 21 intergenic regions in the aflatoxin gene clusters of A. flavus and A. parasiticus revealed significant linkage disequilibrium (LD) organized into distinct blocks. To determine whether sexual reproduction gives rise to recombination blocks, we tested the null hypothesis of an equal number of MAT1-1 and MAT1-2 in populations sampled from each locality/species using a two-sided binomial test. For both A. flavus and A. parasiticus, when the number of MAT1-1 and MAT1-2 was significantly different in both corrected and uncorrected samples, there was more extensive LD in the cluster and isolates grouped into specific chemotypes, either the nonaflatoxigenic class in A. flavus or the B1-dominant and G1-dominant classes in A. parasiticus. In A. flavus, a 1:1 distribution of MAT genes reduces the frequency of nonaflatoxigenic strains and increases the resolution of LD blocks. In A. parasiticus, sexual reproduction and recombination reduces the frequency of B1-dominant and G1-dominant chemotypes, and isolate G1/B1 ratios show a continuous distribution in the population.