Mycotoxins are fungal secondary metabolites that are harmful to the health of humans and/or animals. Aflatoxins, trichothecenes (T-2 toxin and DON toxin) and fumonisins are the major mycotoxins that contaminate crop plants and, as a result, are of great importance to agricultural economics and in food and feed safety. Aflatoxins are produced mainly by the two Aspergillus species in section Flavi, A. flavus and A. parasiticus. Sterigmatocystins (precursor of aflatoxins) are produced by some strains of A. nidulans. Trichothecenes and fumonisin are produced by Fusarium species. In the genus Aspergillus, the nonaflatoxin-producing species A. fumigatus, which is a human pathogen; A. oryzae and A. sojae, which are used in food fermentation, and A. niger, which is used in industrial fermentation, are close relatives of aflatoxin-producing species A. flavus and A. parasiticus. The genetics and biology of aflatoxin, trichothecene and fumonisin biosynthesis have been investigated in significant detail, and many of the genes and/or enzymes involved in toxin formation have been identified. Genomic efforts, such as Expressed Sequence Tag (EST), cosmid clone sequencing, chromosome sequencing, and large-scale whole genome sequencing, on toxigenic and non-toxigenic Aspergillus and Fusarium species have been made in recent years. The technological breakthroughs in genomics research will almost certainly promote revolution in our understanding of the biology and genetics of these filamentous fungi for the control of mycotoxin contamination in food and feed and for the improvement in yield and quality of industrial fermentation products. In this chapter, we review advances in genomics research on those Aspergillus and Fusarium species.