Hydrology plays a dominant role in wetland plant distribution and microbial composition, but few studies explicitly attempted to relate the linkage between wetland vegetation and microbial community. The present study consisted of five wetland plant communities along three adjacent flood gradients zones(zone 1 dominated by Carex appendiculat, zone 2 dominated by Eleocharis ovate, and zone 3 dominated by Phragmites australis/Bidens pilosa/Calamagrostis angustifolia, which formed separate, monoculture patches). Gram negative and arbuscular mycorrhizal fungal phospholipid fatty acid(PLFA) are more abundant in the site with short flooding period(zone 3) than in the site with long flooding period(zone 1), and they are also different in the P. australis, B. spilosa and C. angustifolia of zone 3. Principle Component Analysis(PCA) showed that the flooding period could explain 92.4% of variance in microbial composition. Redundancy Analysis(RDA) showed that available nitrogen(AN), total nitrogen(TN) and soil organic matter(SOM) could explain the 79.5% of variance in microbial composition among E. ovata, P. australis, B. pilosa and C. angustifolia. Results demonstrated that flooding period was the main factor in driving the microbial composition and plant-derived resources could influence soil microbial composition in the seasonally flooded zones. The present study consisted of five wetland plant communities along three adjacent flood gradients zones appendiculat, zone 2 dominated by Eleocharis ovate, and zone 3 dominated by Phragmites australis / Bidens pilosa / Calamagrostis angustifolia, which formed separate, monoculture patches. Gram negative and arbuscular mycorrhizal fungal phospholipid fatty acid (PLFA) are more abundant in the site with short flooding period (zone 3) than in the site with long flooding period (zone 1), and they are also different in the P. australis, B. spilosa and C. angustifolia of zone 3. Principle Component Analysis (PCA) showed that the flooding could could 92.4% of variance in microbial composition. Redundancy Analysis (RDA) showed that available nitrogen (AN), total nitrogen (TN) and soil organic matter (SOM) could explain the 79.5% of variance in microbial composition among E. ovata, P. australis, B. pilosa and C. angustifolia. Results demonstrated that flooding period was the main factor in driving the microbial composition and plant-derived resources could influence soil microbial composition in the seasonally flooded zones.