Yangtze estuary, lying in the subtropical monsoon region of China, is characterized by a unique environmental setting and endemic wetland plant species (Scirpus mariqueter). Methane (CH4) emission fluxes were measured at the Yangtze estuarine wetland, Chongming Dongtan (CD), by a static closed chamber technique from May 2004 to April 2005. The results showed that CD is the source of atmospheric CH4, and emission fluxes had significant diurnal and seasonal variation. The annual average CH4 emission flux was 2.06 mg m−2 h−1 at the CD marsh site and 0.04 mg m−2 h−1 at the CD bare tidal flat (nonvegetated). Wetland plant species (S. mariqueter) and temperature were the primary factors controlling the CH4 emission. The results of the light and dark chamber comparison and plant shoot clipping experiment suggest that molecular diffusion and convective gas flow methods were the two main mechanisms of CH4 transported via S. mariqueter plants in July. However, molecular diffusion was believed to be the primary transport mechanism from August to October, with leaf resistance as one of the factors regulating CH4 diffusion. There was significant correlation between CH4 fluxes and temperature, especially the 10 cm depth ground temperature (R2 = 0.7784). Although sediment organic carbon content did not determine CH4 fluxes, net ecosystem production was significantly correlated with CH4 fluxes, suggesting that the photosynthates of S. mariqueter effectively provided the substrate for methanogenic bacteria.