Microorganisms are important components of wetland ecosystem as they play a range of vital ecological functions such as nitrogen fixation, Diazotrophic bacteria associated with the roots of the invasive species Spartina alterniflora play a vital role in the process of plant growth.However, it was unclear whether invasive plant had a powerful impact on the diversity of nitrogen-fixing bacteria.To address this problem, We compared the diversity and abundance of diazotrophs in the rhizosphere soil of the invasive exotic specie (S.alterniflora) and native species (Phragmites australis and Scirpus mariqueter) by method of denaturing gradient gel electrophoresis (DGGE).The results of DGGE analyses of nifH gene fragments showed that the rhizoshpere soil of S.alterniflora contains diazotrophs more diversely.Canonical correspondence analysis (CCA) revealed that total Kjeldahl nitrogen, ammonia nitrogen and organic phosphorus accounted for a significant amount of the diazotrophs.In this study, a total of 46 sequences were recovered and cloned, and were aligned with sequences from cultured and uncultured diazotrophs in order to determine the types of organisms present in the Spartina rhizosphere.The result of this study indicated most sequences as uncultured and gamma-Proteobacteria, and some were characterized into the members of genera Azotobacter, Ectothiorhodospira, Methylococcus, Frankia, Agrobacterium, Geobacter, Pseudomonas, Bradyrhizobium and Azospirillum.The result indicated that diazotrophs assembling in the Spartina rhizosphere had enormous diversity, and the same results did not appear in the native plants and mudflat.The foreign species S.alterniflora promoted the diversity of rhizosphere nitrogen-fixing microorganisms and the active activities of nitrogen-fixing microorganisms can be concluded as an important factor of Spartina mechanisms.