Technical Abstract: Aspergillus flavus is a pathogen that infects plants, animals, and humans. It produces the most potent carcinogens, known as aflatoxins, when it infects agricultural crops. In order to devise strategies to control aflatoxin contamination of pre-harvest agricultural crops and post harvest grains during storage, we launched the A. flavus genomics program. The objectives are to identify genes involved in aflatoxin biosynthesis and to understand the mechanisms of its genetic regulation, as well as fungal pathogeneicity. The A. flavus whole genome sequencing has been completed. Initial annotation of the sequence revealed that there are about 13 071 genes in the A. flavus genome. Genes which potentially encode for enzymes involved in secondary metabolite production in the A. flavus genome have been identified. Preliminary comparative genome analysis of A. flavus with A. oryzae is summarized.