To research the effect of cotton soil microorganisms, the genetic diversity of 58 aerobic nitrogen-fixing bacteria isolated from cotton soils in Yangtze River were studied by ERIC-PCR and the 16S rDNA sequence analysis. The ERIC-PCR results showed that tested strains formed 9 clusters defined by 0.65 of Watson distance. The type strains of 6 cluster were identified as Enterobacter, Bacillus, Acinetobacter, Pseudomonas, Serratia, Yersinia by 16SrDNA sequencing analysis.