Soil salinity is a major production constraint and even moderate salinity levels can severely impair rice yields. Metabolomic profiles represent a functional readout of cellular biochemistry, thus more closely correlating with the phenotype than the transcriptomics or proteomics. In an effort to identify metabolic basis of salt tolerance in rice, we compared metabolic profiles between salt-tolerant Pokkali and salt-sensitive IR29. This analysis has revealed that the abundances of several metabolites significantly differed between genotypes and between roots and shoots. Importantly, serotonin accumulation under salinity was remarkably elevated in Pokkali. Serotonin biosynthesis is controlled by tryptophan decarboxylase (TDC) and tryptamine hydroxylase (T5H) in rice. To examine correlations between serotonin accumulation and its’ biosynthesis, the expression analysis for TDC and T5H genes are being performed under stress conditions in these two rice genotypes. To further define the genetic basis of importance of serotonin in salt tolerance of rice, we are characterizing and assaying mutants that are defective in serotonin accumulation or overproducing it.