Chinese rice wine is mainly produced in the southern region of China, such as Shaoxing city in Zhejiang province, Shanghai city and Jiangsu province. Baipu rice wine is a typical representative of Chinese cleanlily type rice wine, whose aromas and flavours are significantly different from those of Shanghai rice wine and Zhejiang rice wine. Wheat Qu as saccharifying and fermenting agent is the main reason to cause the flavour differences of rice wine. The fungal community structure of Nantong Baipu rice wine wheat Qu was studied using conventional dilution plate method and a culture independent method, combining with ITS sequence analysis, and was compared with the microbial community structure of Shaoxing rice wine wheat Qu. Eleven different kinds of filamentous fungi were. The main moulds in Baipu rice wine wheat Qu after being isolated and identified were Cladosporium cladosporioides, Aspergillus candidus, Aspergillus oryzae, Penicillium granulatum and Penicillium chrysogenum, whose concents were 24%, 25%, 6%, 18% and 22%, respectively. The filamentous fungi of Shaoxing rice wine wheat Qu were reported to be Absidia corymbifera, Rhizopus oryzae, Rhizomucor Pusillu, Aspergillus orgyze, Aspergillus fumigatus and a little of Penicillium sp., which were greatly distinct compared with Nantong Baipu rice wine wheat Qu.