Mycotoxins are biochemical compounds or secondary metabolites produced by numerous fungal pathogens. These are hazardous compounds and unsafe for plants, humans and animals and can cause diseases or death. On the basis of food toxicity, mycotoxins are grouped in five major groups: aflatoxins, ochratoxin, fumonisins, deoxynivalenol/nivalenol and zearalenone. Some important fungal species such as Aspergillus, Fusarium and Penicillium are the major fungal groups which produce most of mycotoxins. Based on availability of mycotoxins in food, the fungi have been divided in two groups: field fungi, which attack the crop and fungal mycotoxins that attack before harvest and storage fungi, which occur only after harvest. Almost every crop is infected with numerous types of fungal mycotoxins, and nearly 25% of crops are affected with fungi worldwide. Maize is one of the most highly susceptible crops, whereas rice is least susceptible to mycotoxins. Due to their harmful effects on plant and animals, it is necessary to remove or manage the development and production of mycotoxins. Several strategies have been developed to manage mycotoxin production including breeding resistant varieties, chemical control and cultural control. Resistant plants provide an effective and environmentally friendly approach to managing mycotoxins. Several more methods have also been developed to manage mycotoxins including conventional methods (spectrometry, HPLC, chromatography, ELISA), advanced methods (DNA sensor-based and nanoparticle-based methods) and on-site detection methods using some kind of strip-based sensor and some field chip-based methods. Mycotoxins are expected to become a greater concern for the feed and food supply chains in the future.