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Invasion of introduced lineage of common reed (Phragmites australis) into water-saturated communities in the Great Plains has modified habitats and ecosystem services. In several areas it grows alongside and out-competes its native counterpart. We investigated ecophysiological responses of the two lineages to nitrogen (N) fertilization and temperature (19°, 25°, and 32°C). Photosynthesis (Amax) did not differ between lineages at temperatures of 19° and 25°C but was higher in the native lineage at 32°C. Fertilization improved Amax at all temperatures, and was more pronounced in the native than in the introduced lineage. Native P. australis had higher δ13C and water use efficiency (wue) compared to the introduced lineage. Differences in maximum photochemical efficiency of photosystem II (Fv/Fm), carboxylation efficiency (Vcmax), and electron transport (Jmax) were observed between lineages, and generally responded positively to treatments. Our results indicated that the native P. australis may better withstand water fluctuations and warmer temperatures than its introduced counterpart, and could contribute to diverse plant communities under warmer climate scenarios. In contrast, under cool temperatures, the introduced lineage has an advantage that could lead to further displacement of native species in water-saturated communities.