Abstract: To understand the adaptability of fungi in rhizosphere soil of soybean, two saline-alkali stress ways were set which involved irrigating saline solution (A) and covering saline soil (B), to analyze the diversity of rhizospherical fungi of wild soybean and cultivated soybean, throughthe application of DGGE method. The results showed that the saline alkali stress ways had great influence on the similarity of fungi in rhizosphere of soybean. For example, under the same saline alkali stress way and concentration of A₁, the similarity ratio between the rhizospherical fungi of wild soybean and cultivated soybean was 0.70. In addition, appropriate saline concentration can increase the uniformity and Shannon index of soybean rhizospherical fungi, for example, the uniformity of wild soybean at concentration of B₁ was 0.99, and the Shannon index at concentration of A₂ was 1.87. Moreover, the sequencing of DGGE specific bands and the further comparison with gene bank, some comparative advantageous strain were obtained, such as Fusarium oxysporum, Actinomucor elegans, Marcelleina tuberculispora, Marcelleina persoonii, Tofieldiaceae environmental sample clone and Uncultured eukaryote clone etc.