Abstract: Soil microbial community is an important indicator for assessing changes in soil quality, fertility and soil environment. Fertilization and groundwater table are two factors that may affect soil fertility and micro-environment. However, so far little has been reported on influence of groundwater table on soil microbial community, especially the joint effects of fertilization and groundwater table on soil microbial community. Phospholipid fatty acids (PLFA) analysis was conducted to evaluate impacts of fertilization and groundwater table on the soil microbial community in a red soil rice paddy. Results show that groundwater table significantly influenced soil pH, E_h,p (oxido-reduction potential in drained soil) and NO₃^- content, while soil fertilization did significantly soil E_h,y (oxido-reduction potential in flooded soil), E_h,p, total organic carbon, total N and available K contents. Besides, groundwater table significantly affected contents of total PLFA, bacterial PLFA, and Gram-positive (G⁺) bacterial PLFA and G⁺ PLFA/G^- PLFA ratio while fertilization did significantly content of Gram-negative (G^-) bacterial PLFA contents and G⁺ PLFA/G^- PLFA ratio of the soil microbial community. Stepwise regression analysis shows that soil pH and total nitrogen content significantly affected actinomycete PLFA content, and soil pH did significantly contents of G⁺ bacterial PLFA, aerobic and anaerobic bacterial PLFA, too; soil E_h,y did significantly fungal to bacterial PLFA ratio; and contents of NO₃^--N and total K nitrogen did significantly G⁺ PLFA/G^- PLFA ratio. PCA analysis shows that the environmental factors significantly affected soil microbial structure, total K, pH and E_h,y of the soils under long-term fertilization and varying groundwater table, thus making Treatment LNOM different from the other treatments, while NO₃^--N, total N and total P contents were the important factors making Treatments HNOM, HHOM, LCF, HCF and LHOM different from each other in microbial community. Obviously long-term fertilization and groundwater table significantly affect physiochemical properties and soil microbial community in the soil.