Spartina alterniflora, a perennial grass with C(4)-photosynthesis, shows great invading potential in the coastal ecosystems in the east of China. We compared trace gas emissions from S. alterniflora with those from a native C(3) plant, Phragmites australis, by establishing brackish marsh mesocosms to experimentally assess the effects of plant species (S. alterniflora vs. P. australis), flooding status (submerged vs. non-submerged), and clipping (plants clipped or not) on trace gas emissions. The results show that trace gas emission rates were higher in S. alterniflora than P. australis mesocosms due to the higher biomass and density of the former, which could fix more available substrates to the soil and potentially emit more trace gases. Meanwhile, trace gas emission rates were higher in non-submerged than submerged soils, suggesting that water might act as a diffusion barrier in the brackish marsh mesocosms. Interestingly, methane (CH(4)) emission rates were lower in clipped non-submerged mesocosms than in non-clipped submerged mesocosms, but nitrous oxide (N(2)O) emissions were enhanced. CH(4) emissions were significantly correlated with the plant biomass and stem density (R(2)>0.48, P<0.05) for both species, suggesting that both the two species might play important roles in CH(4) production and transport and also act as suppliers of easily available substrates for the methanogenic bacteria in wetland ecosystems. N(2)O emissions, however, were not significantly correlated with plant biomass and density (P>0.05).