The replacement of native species by invasive Phragmites australis in coastal wetlands may impact ecosystem processes including fluxes of the greenhouse gases (GHGs) carbon dioxide (CO 2 ) and methane (CH 4 ). To investigate differences in daytime CH 4 and CO 2 fluxes as well as vegetation properties between Phragmites and native vegetation zones along a salinity gradient, fluxes were measured via cavity ringdown spectroscopy in 3 New England coastal marshes, ranging from oligohaline to polyhaline. While daytime CH 4 emissions decreased predictably with increasing soil salinity, those from Phragmites zones were larger (15 to 1254 μmol m −2 h −1 ) than those from native vegetation (4-484 μmol m −2 h −1 ) across the salinity gradient. Phragmites zones displayed greater daytime CO 2 uptake than native vegetation zones (−7 to −15 μmol m −2 s −1 vs. -2 to 0.9 μmol m −2 s −1 ) at mesohaline-polyhaline, but not oligohaline, sites. Results suggest that vegetation zone and salinity both impact net emission or uptake of daytime CO 2 and CH 4 (respectively). Future research is warranted to demonstrate Phragmites-mediated impacts on GHG fluxes, and additional measurements across seasonal and diel cycles will enable a more complete understanding of Phragmites' net impact on marsh radiative forcing.