To understand the characteristics of fungal community structure in the lesion tissues of Kuerle fragrant pear "Blackhead Disease", the fungal community structure of 12 samples from 4 different fresh-keeping storage in Kuerle area is studied using PCR-DGGE technique. Biodiversity is analyzed by DGGE fingerprint. The results indicat that there is some differencs in the community structure of all samples，which may be related to the planting environment. The 9th stripe in different samples has the highest dominance in the whole the lesion process. The representative strains can be considered as the main pathogenic bacteria in Korla pear "blackhead disease". According to the results of sequence analysis of DGGE dominant bands，it is phylogentically close to Alternaria. It preliminary reveals the variation regular of microbial communities in Korla fragrant pear diseased tissues，which provides a theoretical basis for studies of "Blackhead Disease" in Korla fragrant pear.
