To investigate the fungal diversity in medicinal and edible Coicis Semen,thus providing evidence for its safe use.Methods:A total of 18 batches of Coicis Semen samples were collected.The total DNA was extracted,and the ITS2 sequences were amplified.Then,the amplicons were sequenced using the Illumina MiSeq PE250 platform.Results:The fungi detected were denominated to 4 phylum,18 class,44 orders,99 families,and 149 genera.Ascomycota was the dominant fungus at the phylum level.At the genus level,Fusarium was the most predominant,followed by Aspergillus,Beauveria,Alternaria,Arachnomyces and Penicillium,accounting for (3.05%～60.32%),(2.20%～45.44%),(0.07%～63.21%),(0.80%～11.92%),(0.03%～39.36%) and (0.24%～8.03%).In addition,a total of 5 potential mycotoxin-producing fungi were detected,namely,A.fumigatus,A.terreus,F.poae,P.capsulatum and P.paxillin.Conclusion:High-throughput sequencing technology can quickly and effectively detect fungal contamination in Coicis Semen,thereby providing early warning for mycotoxin contamination in Coicis Semen.