Mycotoxin producing capability greatly varies within species. In theory, the major source of this variability is meiotic recombination. However, a number of important toxigenic species have no known sexual stage and, therefore, the origin of the intraspecific diversity in these fungi is poorly understood. Mating in sexually reproducing Ascomycetes is controlled by MAT genes, but fungi with no known sexual stage also may have fully functional, constitutively transcribed mating type genes. The MAT genes, MAT1-1-1 and MAT1-2-1 encode putative transcription factors which, besides regulating pheromone and pheromone receptor genes, may affect other genes not involved directly in the mating process. By comparing the transcript profiles of a DeltaMAT1-2-1 knock-out mutant and the wild type of Fusarium verticillioides, more than 200 ESTs, either down- or up-regulated in the mutant, were identified. Sequences encoding proteins involved in protein synthesis and metabolism occurred more frequently among ESTs up-regulated in the mutant, while sequences involved in cell signaling and communication were more frequent in the down-regulated subset of ESTs. The lack of fertility in fungi with no known sexual stage and the limited fertility of local populations of sexually reproducing fungi are probably due to changes in one or more of numerous genes that cause female sterility. A number of gene disruption mutants of Fusarium proliferatum were assessed for their mating capabilities. Fphch (a Het-C homologue), Fpmtr (an amino acid transporter gene), and Fpnitr1 (a putative nitrilase encoding gene) encode proteins in seemingly unrelated pathways, but mutations at any of these loci can reduce female fertility. Thus, a number of genes, with functions not related directly to mating, can influence the frequency of sexual reproduction indicating that this process requires the concerted operation of many factors not obviously connected to female fertility/sterility.