Denaturing　gradient　gel　electrophoresis　(DGGE)　has　become　a　widely　used　tool　to　examine　microbial　community　structure.　However,　when　DGGE　is　applied　to　evaluate　the　fungal　community　of　traditional　fermentation　starters,　the　choice　of　hypervariable　ribosomal　RNA　gene　regions　is　still　controversial.　In　the　current　study,　several　previously　published　fungal　PCR　primer　sets　were　compared　and　evaluated　using　PCR-DGGE,　with　the　purpose　of　screening　a　suitable　primer　set　to　study　the　fungal　community　of　traditional　fermentation　starters　for　Hong　Qu　glutinous　rice　wine.　Firstly,　different　primer　sets　were　used　to　amplify　different　hypervariable　regions　from　pure　fungal　cultures.　Except　NS1/FR1　+　and　ITS1fGC/ITS4,　other　primer　sets　(NL1　+　/LS2R,　NL3A/NL4GC,　FF390/FR1　+,　NS1/GCFung,　NS3　+　/YM951r　and　ITS1fGC/ITS2r)　amplified　the　target　DNA　sequences　successfully.　Secondly,　the　selected　primer　sets　were　further　evaluated　based　on　their　resolution　to　distinguish　different　fungal　cultures　through　DGGE　fingerprints.　Three　primer　sets　(NL1　+/LS2R,　NS1/GCFung　and　ITS1fGC/ITS2r)　were　finally　selected　for　investigating　the　fungal　community　structure　of　different　traditional　fermentation　starters　for　Hong　Qu　glutinous　rice　wine.　The　internal　transcribed　spacer　(ITS)　region　amplified　by　ITS1fGC/ITS2r,　which　is　more　hypervariable　than　the　18S　rRNA　gene　and　26S　rRNA　gene,　provides　an　excellent　tool　to　separate　amplification　products　of　different　fungal　species.　Results　indicated　that　PCR-DGGE　profile　using　ITS1fGC/ITS2r　showed　more　abundant　fungal　species　than　that　using　NL1　+/LS2R　and　NS1/GCFung.　Therefore,　ITS1fGC/ITS2r　is　the　most　suitable　primer　set　for　PCR-DGGE　analysis　of　fungal　community　structure　in　traditional　fermentation　starters　for　Hong　Qu　glutinous　rice　wine.　DGGE　profiles　based　on　ITS1fGC/ITS2r　revealed　the　presence　of　twenty-four　fungal　species　in　traditional　fermentation　starter.　A　significant　difference　of　fungal　community　can　be　observed　directly　from　DGGE　fingerprints　and　principal　component　analysis.　The　statistical　analysis　results　based　on　the　band　intensities　of　fungal　DGGE　profile　showed　that　Saccharomyces　cerevisiae,　Saccharomycopsis　fibuligera,　Rhizopus　oryzae,　Monascus　purpuretts　and　Aspergillus　niger　were　the　dominant　fungal　species.　In　conclusion,　the　comparison　of　several　primer　sets　for　fungal　PCR-DGGE　would　be　useful　to　enrich　our　knowledge　of　the　fungal　community　structures　associated　with　traditional　fermentation　starters,　which　may　facilitate　the　development　of　better　starter　cultures　for　manufacturing　Chinese　Hong　Qu　glutinous　rice　wine.