North American wetlands have been invaded by an introduced lineage of the common reed, Phragmites australis. Native lineages occur in North America, but many populations have been extirpated by the introduced conspecific lineage. Little is known about how subtle changes in plant lineage may affect methane (CH 4 ) emissions. Native and introduced Phragmites were grown under current and predicted future levels of atmospheric CO 2 and nitrogen(N) pollution in order to understand how CH 4 emissions may vary between conspecific lineages. We found introduced Phragmites emitted more CH 4 than native Phragmites, and that CH 4 emissions increased significantly in both with CO 2 +N treatment. There was no significant difference in CH 4 production potentials, but CH 4 oxidation potentials were higher in soils from the introduced lineage. Intraspecific plant responses to resource availability changed CH 4 emissions, with plant density, root mass, and leaf area being significantly positively correlated with higher emissions. The absence of CO 2 -only or N-only effects highlights a limitation on the generalization that CH 4 emissions are proportional to plant productivity. Our data suggest that intraspecific changes in plant community composition have important implications for greenhouse emissions. Furthermore, global change-enhanced invasion by introduced Phragmites may increase CH 4 emissions unless these factors cause a compensatory increase in carbon sequestration.