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 (CO2) and methane (CH4). To investigate differences in daytime CH4 and CO2 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 CH4 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 CO2 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 CO2 and CH4 (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.