Mycotoxins are the secondary metabolites of fungi which are related to specific issue in animals and human and recognize an overall issue influencing staple harvests. The accurate identification of mycotoxigenic fungi stills one of the most basic zones for mycological ordered exploration on account of the significance of mycotoxins and to some degree befuddle condition of the systematic. The utilization of PCR to distinguish mycotoxigenic fungi is drawing into extensive consideration. These techniques depend on the isolation of genes responsible for mycotoxin biosynthesis. In general, only a couple of mycotoxins which their natural chemistry was resolved adequately to empower the improvement of the probes of the gene pathway. The basic of PCR analysis was described as the alternative assay because the microbiological and chemical methods for detection and identification of mycotoxigenic fungi are time cumbersome and time-consuming. For a viable distinguishing proof of utilization to the food manufacture and to avoid misidentification, probably it is more valuable to think about a collection of isolates grouped as a single taxon that can produce mycotoxin. So, this review is aiming to explore the PCR as a promising, specific, and reliable technique for the identification of mycotoxigenic fungi e.g., aflatoxigenic, ochratoxigenic, and mycotoxigenic Fusarium species.