Conversion of land from wetland to agricultural management practices can lead to significant changes in nutrient rich topsoil, which may have an impact on microbial community structure in soils. However, little is known about how long-term (ca. 40 years) rice cultivation, one of major agricultural management practices in many regions, influence soil microbial biomass and community structure. Soil samples were collected from a wetland and paddy field in Anhui province in eastern China to examine soil physical and chemical characteristics and associated soil microbial biomass and community composition. Microbial community composition was assessed using phospholipid fatty acid (PLFA) analysis, terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes. Results indicated that soil moisture content, pH, soil organic carbon, total nitrogen and NH4[^+]-N contents were significantly lower in the paddy field in comparison to the wetland. Total microbial biomass showe showed a slightly significant decrease in the paddy field, however, there were significant shifts in the composition of the microbial communities based on the PLFA and T-RFLP fingerprintings in the both ecosystems. Signature PLFA analysis revealed that the sum of bacterial PLFAs and the relative proportions of Gram negative bacterial specific PLFAs significantly decreased in the paddy field, nonetheless, the relative numbers of actinobacterial, Gram positive and fungal PLFAs as well as the ratio between the bacterial and fungal PLFAs were not affected by the long-term agricultural management. These results revealed that long-term rice cultivations not only drastically decreased soil nutrients but also leaded to shifts in the soil microbial community structure, which would be helpful to provide a better understanding of wetland conservation and management practices.