Abstract: Abstract: In order to investigate the mechanism of methane emission based on different water management and rice straw returning, this study determined the CH4 flux and the abundance and community structure of methanogens and methane oxidizing bacteria. Quantitative polymerase chain reaction (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) were used to determine the abundance and community composition of mcrA-containing methanogens and pmoA-containing methane oxidizing bacteria in DNA and cDNA level from paddy field. The soil samples taken from the paddy soil at Changsha Research Station for Agricultural & Environmental Monitoring of Institute of Subtropical Agricultural, the Chinese Academy of Sciences. Four treatments included the following: CF (balanced fertilizer without rice straw returning and long-term flooding), HS+CF (balanced fertilizer with 6.0 t/hm2 rice straw returning and long-term flooding), IF (balanced fertilizer without rice straw returning and intermittent irrigation), HS+IF (balanced fertilizer with 6.0 t/hm2 rice straw returning and intermittent irrigation). The results showed that long-term flooding significantly increased methane emissions, but not rice straw returning. And there was no significant interaction between the treatments of water management and rice straw returning. The community structure of methanogens and methane oxidizing bacteria were affected by water management, but not by rice straw returning based on cluster analysis. At the level of cDNA, the community structure of methanogens and methane oxidizing bacteria were different between the treatments of long-term flooding and intermittent irrigation under the condition with or without rice straw returning. While, at the level of DNA, the communities structure were only affected by water management under the condition without water management. At the T-RFLP profile, there were obviously difference between the community structure at DNA level and transcriptional community structure at cDNA level of methanogens and methane oxidizing bacteria, which were more sensitive to water management at cDNA level than that at DNA level. The abundance of methanogens were affected by water management and rice straw returning at cDNA and DNA level, but not of methane oxidizing bacteria. CH4 emissions significantly correlated with the ratio of the abundance of mcrA and pmoA genes at DNA level, not with the abundance of mcrA or pmoA genes. So the CH4 emissions determined by the ratio of the abundance of methanogens and methane oxidizing bacteria, not of methanogens or methane oxidizing bacteria. In totally, the community structure and abundance of methanogens and methane oxidizing bacteria is more affected by water management than rice straw returning based on the short-tern experiment. The community structure and abundance of methanogens and methane oxidizing bacteria are affected by water management at DNA and cDNA level. The ratio of the abundance of mcrA and pmoA genes is the key to control the methane emissions from paddy field.