To explore fungal community structure and species composition in the pile-fermentation process of Fuzhuan brick tea(FBT), the fungal variable region of 18S rDNA was amplified in different periods of pile-fermentation process. Amplified products were separated by denaturing gradient gel electrophoresis (DGGE) and the bands were cloned, sequenced and aligned. The results showed that fungal species were rich in pilefermentation process of FBT, including Wallemia sebi, Candida sp., Candida tropicalis, Lodderomyces sp., Debaryomyces hansenii, Pichia kudriavzevii, Saccharomyces cerevisiae, Cryptococcus sp., Rhodotorula graminis, Eurotium amstelodami, Aspergillus glaucus, Rhizomucor miehei, Rhizomucor pusillus, Galactomyces geotrichum, Candida ontarioensis, Trichosporon dermatis, Penicillium decumbens and Aspergillus penicillioides. Two distinctive kinds of fungal communities, correlating to the pile-fermentation times: 0 –24 h and >24 – 48 h, were found. The fungi Shannon-Wiener Index gradual tended to increase during 0 –16 h in pile-fermentation process of FBTand to reduce slightly during >16 –24 h, it reached to the maximum 2.348 after 40 h, and still maintained the higher level during >40 – 48 h. The dominant fungi were Lodderomyces sp. and Debaryomyces hansenii, the sub-dominant were Eurotium amstelodami throughout the pile-fermentation process of FBT, and sub-dominant fungi, Wallemia muriae, Debaryomyces hansenii and Saccharomyces cerevisiae were appeared in the later of pile-fermentation. The 18S rDNA alignment results also proved that there were three strains Wallemia sebi and 7 strains Eurotium amstelodami, which indicated that a wide variety of subspecies and ecotype existed in the dominant fungi. This study showed a detailed spectrum of fungi at different time periods during the pile-fermentation process. DGGE fingerprint, a novel technique could obtain a comprehensive, detailed fungal community structure and variation in the pile-fermentation process of FBT.