The aim of this investigation was to compare the transcriptional expression of starch metabolism, involving genes and physiological characters, in seedlings of two contrasting salt-tolerant rice genotypes, in response to saltstress. The soluble sugar content in rice seedlings of both salt-tolerant and salt-sensitive genotypes was enriched, relating to starch degradation, in plants subjected to 200 mM NaCl. In the salt-tolerant cultivar Pokkali, a major source of carbon may be that derived from the photosynthetic system and starch degradation. In starch degradation, only Pho and PWD genes in Pokkali were upregulated in plants subjected to salt stress. In contrast, the photosynthetic abilities of IR29 salt-susceptible cultivar dropped significantly, relating to growth reduction. The major source of carbohydrate in salt-stressed seedlings of the IR29 cultivar may be gained from starch metabolism, regulated by ADP-glucose pyrophosphorylase (AGP), starch synthase (SS), starch branching enzyme (SBE), starch debranching enzyme (ISA), glucan-water dikinase (GWD), dispropotionating enzyme (DPE), phospho glucan-water dikinase (PWD) and starch phosphorylase (Pho). Also, the major route of soluble sugar in salt-stressed Pokkali seedlings was derived from photosynthesis and starch metabolism. This was identified as novel information in the present study.