This paper summarized the research progress made in molecular identification methods for toxigenic fungi, which can produce aflatoxin, ochratoxin, trichothecenes, fumonisin, zearalenone or patulin, etc. Compared with the traditional diagnoses for morphology and physiology identification, the molecular identification is more simple, quick and accurate. It can provide technological support for early-stage warning on the harm caused by mycotoxin-producing fungi and is of very important and realistic significance for effective prevention and control of mycotoxin contamination.