Application of mycorrhizal inoculum could be one way to increase the yield of rice plants, and reduce the application of fertilizer. We therefore studied arbuscular mycorrhizal fungi (AMF) in the roots of wetland rice (Oryza sativa L.) collected at the seedling, tillering, heading and ripening stages in four paddy wetlands that had been under a high-input and intensively irrigated rice cultivation system for more than 20 years. It was found that AMF colonization was mainly established in the heading and ripening stages. The AMF community structure was characterized in rhizosphere soil and root from two of the studied paddy wetlands. A fragment covering partial SSU, the whole ITS and partial LSU rRNA operon region of AMF was amplified, cloned and sequenced from roots and soils. A total of 639 AMF sequences were obtained, and these were finally assigned to 16 phylotypes based on a phylogenetic analysis, including 12 phylotypes from Glomeraceae, one phylotype from Claroideoglomeraceae, two phylotypes from Paraglomeraceae and one unidentified phylotype. The AMF phylotype compositions in the soils were similar between the two surveyed sites, but there was a clear discrepancy between the communities obtained from root and soil. The relatively high number of AMF phylotypes at the surveyed sites suggests that the conditions are suitable for some species of AMF and that they may have an important function in conventional rice cultivation systems. The species richness of root-colonizing AMF increased with growth of rice, and future studies should consider the developmental stages of this crop in the exploration of AMF function in paddy wetlands.