The study reports the responses of photosynthesis to NaCl stress in two C4 species: a glycophyte Setaria viridis (SV) and a halophyte Spartina alterniflora (SA). SV was unable to survive following exposure to NaCl level higher than 100 mM, in contrast, SA could tolerate NaCl up to 550 mM. Under different O2 concentrations, SV showed an increased P700 oxidation level following NaCl treatment, while SA showed almost no change. We also observed an activation of the NDH-dependent cyclic pathway in SV by about 2.4 times upon exposure to 50 mM NaCl for 12 days; however, its activity in SA dropped by about 25%. Using PTOX inhibitor (n-PG) and inhibitor of the Qo-binding site of Cytb6/f (DBMIB) to restrict electrons flow towards PSI, at either 2% or 21% O2, we showed an enhanced plastid terminal oxidase (PTOX) activity for SA but not for SV under NaCl stress. We further showed that both the mRNA and protein levels of PTOX increased by about 3~4 times for SA under NaCl stress but not or much less for SV. All these suggest that the up-regulation of PTOX is a major mechanism used by halotype C4 species SA to cope with salt stress.