Mold-produced secondary metabolites that are toxic and carcinogenic are termed mycotoxins. They are biosynthesized in a number of fungi, mainly from species in the Aspergillus, Fusarium and Penicillium genera. Mycotoxins contaminate agricultural commodities such as grains, fruits and nuts. Due to their toxic and carcinogenic properties, they pose a serious health hazard to animals and humans and cause staggering economic losses to growers, packers, processors, and consumers annually. Research on major mycotoxins, such as aflatoxins, using molecular biological and genetic tools has uncovered the genes, gene clusters, biosynthetic pathways, and genetic regulatory mechanisms involved in their formation. The field of genomics has empowered scientists with a high throughput tool to study mycotoxin biosynthesis and regulatory networks with a new level of scientific rigor. In this paper, the current status of genomic investigations on mycotoxigenic fungi has been summarized in order to better understand their biosynthesis, genetic regulation, genome structure, and evolutionary aspects. In addition, the advantages, challenges, and future perspectives in studying mycotoxins are discussed. The information and knowledge contained in this chapter may guide possible solutions to abate mycotoxin contamination of agricultural commodities for human consumption and animal feed.