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Pathogenic fungi and mycotoxins threaten plant and animal health and cause economic losses. This book focuses on the recent research progress into pathogenic fungi and mycotoxins in China. The molecular mechanisms of mycotoxin biosynthesis and pathogenic fungi growth and development are reported from the perspectives of transcription regulation, histone modification and enzymes, providing a theoretical basis for discovering new control targets. This Special Issue not only includes a review about the microbial degradation of mycotoxins, but also discusses several new chemical and biological methods which inhibit the biosynthesis of mycotoxin. Special attention is also given to the effect of nutrition on the production of mycotoxins. Some papers have also been collected about detection assays and the risk assessments of mycotoxins. The fundamental and applied research into mycotoxins is not only of particular interest but is also important for reducing economic losses.