As the 20th century ended, Fusarium mycotoxicology entered the age of genomics. With complete genomes of Fusarium graminearum and F. verticillioides and several Fusarium gene expression sequence databases on hand, researchers worldwide are working at a rapid pace to identify mycotoxin biosynthetic and regulatory genes. Seven classes of mycotoxin biosynthetic genes or gene clusters have been identified in Fusarium to date; four are polyketide synthase gene clusters for equisetin, fumonisins, fusarins, and zearalenones. Other Fusarium mycotoxin biosynthetic genes include a terpene cyclase gene cluster for trichothecenes, a cyclic peptide synthetase for enniatins, and a cytochrome P450 for butenolide. From the perspective of the United States Department of Agriculture, the ultimate goal of research on Fusarium molecular biology is to reduce mycotoxins in cereal grains. With this goal in mind, efforts have focused on identifying aspects of mycotoxin biosynthesis and regulation that can be exploited for mycotoxin control. New information on fungal and plant genomes and gene expression will continue to provide information on genes important for fungal-plant interactions and to facilitate the development of targeted approaches for breeding and engineering crops for resistance to Fusarium infection and mycotoxin contamination.