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Understanding the functional relationship between greenhouse gas fluxes and environmental variables is crucial for predicting the impacts of wetlands on future climate change in response to various perturbations. We examined the relationships between methane (CH4) emission and temperature in two marsh stands dominated by the Phragmites australis and Cyperus malaccensis, respectively, in a subtropical estuarine wetland in southeast China based on three years of measurement data (2007-2009). We found that the Q10 coefficient of CH4 emission to soil temperature (Qs10) from the two marsh stands varied slightly over the three years (P > 0.05), with a mean value of 3.38 ± 0.46 and 3.89 ± 0.41 for the P. australis and C. malaccensis stands, respectively. On the other hand, the three-year mean Qa10 values (Q10 coefficients of CH4 emission to air temperature) were 3.39 ± 0.59 and 4.68 ± 1.10 for the P. australis and C. malaccensis stands, respectively, with a significantly higher Qa10 value for the C. malaccensis stand in 2008 (P < 0.05). The seasonal variations of Q10 (Qs10 and Qa10) differed among years, with generally higher values in the cold months than those in the warm months in 2007 and 2009. We found that the Qs10 values of both stands were negatively correlated with soil conductivity, but did not obtain any conclusive results about the difference in Q10 of CH4 emission between the two tidal stages (before flooding and after ebbing). There were no significant differences in both Qs10 and Qa10 values of CH4 emission between the P. australis stand and the C. malaccensis stands (P > 0.05). Our results show that the Q10 values of CH4 emission in this estuarine marsh are highly variable across space and time. Given that the overall CH4 flux is governed by a suite of environmental factors, the Q10 values derived from field measurements should only be considered as a semi-empirical parameter for simulating CH4 emissions.