Soil salinity negatively affects growth and yield of most crop plants. Plants respond to salinity through physiological and biochemical adjustments that involve a coordinate regulation and expression of a cascade of genes. Naturally highly salt tolerant plants, such as halophytes, have been of particular interest to understand the biology of their salt adaptation mechanisms. Spartina alterniflora (smooth cordgrass) is a Louisiana native monocot halophyte that can withstand salinity up to double the strength of sea water. To dissect the genetic mechanisms underlying its salinity adaptation, the leaf and root transcriptome of S. alterniflora, subject to 500 mM NaCl, was sequenced using 454/GS-FLX.