The objective of this study was to investigate the fungal communities in the malting barley.In this paper,nine different DNA extraction methods and the nested PCR-DGGE(nested polymerase chain reaction-denaturing gradient gel electrophoresis) were used.DNA sequencing was proceeded to obtain the dominant fungal population information.The results of nested PCR-DGGE analysis had a sensible difference to different DNA extraction methods.Results showed that total of nine fungi species were detected,including Cochliobolus sativus,Alternaria alternata,Fusarium sporotrichioides,Coniothyrium fuckelii,Aspergillus sp.,Saccharomyces cerevisiae,Sporobolomyces roseus,Cryptococcus magnus,and Entorrhiza fineranae.The study enriched the knowledge of fungal communities in the malting barley,and proved that nested PCR-DGGE was a powerful tool for revealing fungal diversity in the malting barley.