The　selection　of　appropriate　primer　pairs　is　the　crucial　step　in　the　process　of　DGGE　analysis　of　fungal　community　diversity　in　Hong　Qu　glutinous　rice　wine　brewing　system.　A　novel　screening　method　of　PCR-DGGE　primer　pair　was　developed　to　analyze　fungal　community　diversity　in　Hong　Qu　glutinous　rice　wine　brewing　system.　The　approach　is　based　on　sequence　characteristics　of　fungal　community　in　Hong　Qu　glutinous　rice　wine　brewing.　The　optimal　primer　pair　is　determined　through　comparison　of　several　candidate　primer　pairs,　and　the　screening　indicators　include　matching　degree　between　primer　pairs　and　target　sequences,　and　dipartite　degree,　average　difference　degree,　average　sequence　length　and　average　GC　content　of　their　amplified　fragments.　Three　common　fungal　PCR-DGGE　primer　pairs　were　evaluated　by　using　the　novel　screening　method　of　PCR-DGGE　primers　and　DGGE　diversity　analysis,　respectively.　The　results　indicated　that　NSl-Fung　had　a　good　amplification　and　best　dipartite　degree　in　the　two　methods,　which　is　the　optimal　primer　pair　for　studying　fungal　diversity　in　Hong　Qu　glutinous　rice　wine　brewing　system.　Thus,　the　optimal　primer　pair　screened　by　this　method　might　have　very　strong　pertinence,　which　can　avoid　some　of　the　problems　of　those　time　-consuming　and　cumbersome　empirical　procedures　of　multiple　primers　screening　or　combination　strategy.　The　novel　method　can　also　be　guidance　and　reference　for　studying　other　brewing　system　or　microbial　ecology　system.　©　2016,　Editorial　Office　of　Journal　of　CIFST.　All　right　reserved.