Abstract: Long-term continuous cropping of cotton has caused dramatic soil-borne diseases in many places, leading to substantial agricultural losses. However, in some areas of Xingjang Uygur Autonomous Region, the obstacles caused by continuous cotton cropping can spontaneously restore and maintain high yields of cotton for many years. To analyze the variable spectrum of soil fungal communities and changes in the community structure in these spontaneously restored fields during cropping, soils at depths of 1 to 10 cm, 11 to 20 cm, 21 to 30 cm and 31 to 40 cm were sampled from cotton fields with a history of 0 a (unused field), 1 a, 3 a, 5 a, 10 a, 15 a or 20 a of cotton cropping in the Shihezi Region of Xinjiang Uygur Autonomous Region. The fungal communities in these samples were studied using 18S rRNA-based polymerase chain reaction-density gradient gel electrophoresis (PCR-DGGE). Fungal community diversity indices including the Shannon-Wiener diversity index, abundance index and evenness index were compared among these samples. Samples from the unused field had relatively high levels of those three indices. With increasing years of cotton cropping, the fungal abundance, diversity and evenness indices descend, whereas those three indices showed a different decrease in different depth. However, after 10 a of continuous cropping, all these indices were restored to their original values or reached a relative stable level. Cluster analysis of DGGE fragments indicated that the samples of each depth were clustered into different branches. Soil fungi of 21 30 cm plow layer was most significantly affected by continuous cropping. Soil fungi community obviously fluctuated in different depths. Principal component analysis (PCA) showed that at each soil depth, the first two principal components were of the greatest importance and had a combined variance contribution rate >60.1%. Except for the 11-20 cm and 21-30 cm depths of the 1 a continuous cropping soil, all of the cotton soils were positively correlated with the first principal component and fluctuated on the right of the first principal component between the positive and negative axes of the second principal component. Both cluster analysis and PCA results suggested that, compared to that from original uncropped field, the fungal community structure showed the most variation in samples from the depth of 11 30 cm of continuously cropped soils. Twenty-four clones were sequenced and submitted to GenBank (accessory no. JN572633 to JN572656). By aligning with the GenBank database, all sequences from DGGE were classified into three groups: Mitosporic fungi, Uncultured fungi, and Pyronemataceae. Further analysis demonstrated that the isolated sequences showed a homology of 98.5% 100% to known sequences in GenBank and 100% of the sequences belonged to fungium which were not cultured. No microbial data were correlated with soil-borne plant diseases of cotton. The study demonstrated that the age of cotton fields had significant effects on soil fungal diversity. Continuous cotton cropping exerted significant influences on the community structure of soil fungus in Xinjiang Uygur Autonomous Region, with an initial suppression effect on fungal diversity. However, the fungal community reached a stabilized level or a new balance compared with its original state after 10 a of continuous cropping.