In　this　study,　ten　typical　Hong　Qu　samples,　including　five　GuTian　Qu　and　five　WuYi　Qu,　were　collected　for　the　analysis　of　the　fungal　structure,　by　utilizing　culture-independent　molecular　biological　methods.　Through　the　PCR-DGGE　analysis,　it　was　revealed　that,　compared　with　GuTian　Qu,　WuYi　Qu　had　higher　species　richness,　diversity　and　evenness.　Moreover,　via　Principal　Component　Analysis　and　Cluster　Analysis,　it　was　found　that　there　was　significant　difference　of　fungal　structure　between　these　two　types　of　Hong　Qu.　The　predominant　fungi　in　the　starters,　including　Monascus　purpureus,　Aspergillus　flavus,　Rhizopus　oryzae,　Saccharomyces　cerevisiae,　were　also　enumerated　with　Real-Time　PCR　approach.　It　was　determined　that,　M.　purpureus　counts　in　GuTian　Qu　and　WuYi　Qu　were　(6.07　±　0.25)　lg　(CFU/g)　and　(5.82　±　0.11)　lg　(CFU/g),　respectively,　which　without　significant　difference　(P＞0.05).　However,　dramatic　difference　of　the　populations　of　A.　flavus,　R.　oryzae,　S.　cerevisiae　in　these　two　types　of　Hong　Qu　were　found　(P＜0.05).　For　GuTian　Qu,　the　populations　of　A.　flavus,　R.　oryzae　and　S.　cerevisiae　were　(5.94　±　1.04)　lg　(CFU/g),　(4.65　±　0.91)　lg　(CFU/g)　and　(3.33　±　0.99)　lg　(CFU/g),　respectively.　For　WuYi　Qu,　the　populations　of　A.　flavus,　R.　oryzae　and　S.　cerevisiae　were　(8.21　±　1.22)　lg　(CFU/g),　(6.71　±　1.27)　lg　(CFU/g)　and　(5.41　±　0.44)　lg　(CFU/g),　respectively.　In　conclusion,　Hong　Qu　have　a　complex　fungal　diversity,　with　M.　purpureus　as　the　most　predominant　fungi.　This　study　provided　a　detailed　insight　into　the　fungal　community　of　Hong　Qu.　©　2019,　Editorial　Office　of　Journal　of　CIFST.　All　right　reserved.