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The soil microbial assemblages in coastal region is strongly influenced by a wide variety of factors, such as vegetation types and tides. In order to examine the influence of Spartina alterniflora, an exotic species, on the soil microbial assemblages, comparative pairs of experiments were conducted of soil from S. alterniflora marshes and Suaeda salsa marshes for collecting data on soil characteristics, quantity of bacteria, fungi, actinomycetes and azotobacters per gram of dried soil and denaturing gradient gel electrophoresis (DGGE) band profiles. The results revealed that S. alterniflora depressed not only the quantity of microorganisms but also the richness of bacterial community. And, it might suggest that the microbial assemblages were more influenced by vegetation types than tides. Thus, we proposed that the introduction of S. alterniflora into Chinese coastal region should be forbidden.