Setaria viridis seeds and seedlings were subjected to saline and alkaline stress to determine their effect on germination and growth indices, and physiological parameters.The treatments consisted of solutions of NaCl∶Na2SO4 for saline stress and NaHCO3∶Na2CO3 for alkaline stress, at different concentrations.Germination, growth,photosynthesis, chlorophyll fluorescence and ionic balance were determined to elucidate the difference in the mechanism of saline and alkaline stress damage to S.viridis seedlings, and their physiological adaptive mechanism to stress.Germination indices decreased and, germ and root growth were severely inhibited with increased concentrations especially under alkaline stress.We also found that alkaline stress had a more severe effect on S.viridis seedlings than saline stress, which was demonstrated by greater reduction in Relative Growth Rate, Water Content and root system activity.Similarly, the reduction in photosynthesis and chlorophyll fluorescence was greater under alkaline than saline stress.Alkaline stress also appeared to exacerbate the ionic imbalance generated by saline stress; alkaline stress caused a heavy precipitate of phosphate and metal ions, excluding Na+ and K+, and the loss of NO3-and H2PO4-, which caused a sharp decrease in ionic activity and free concentrations of various ions.Our results suggest that damage caused by alkaline stress might come from greater influx of Na+ than caused by saline stree.S.viridis responds by synthesizing greater amounts of organic acids than required to counter salinity to address the intracellular ion imbalance; this process is at the cost of the plants already diminished energy resource.