Kosteletzkya virginica L. Presl. is an obligate wetland species indigenous to southeastern US. Its niche in salt marsh foretells its high salinity tolerance. cDNA-AFLP technique was used to identify the gene transcriptional profiles of leaves and roots from K. virginica seedlings under salt stress in order to clarify the molecular architecture of stress tolerance in the dicot halophyte. Expression analysis over time intervals and under various salt stresses in leaves or roots showed that the quantitatively expressed pattern (in which genes were quantitatively up- or down-regulated under salt stress or fluctuate with different NaCl concentrations) was more prevalent than the qualitatively expressed pattern (in which genes were induced or silenced under salt stress) in K. virginica seedlings under salt stress. The qualitative pattern was appreciably more predominant than the quantitative one only in roots when exposed to salt stress for 2 h. Although each expression pattern was observed in leaves as well as in roots, the percentage of genes (i.e., up-/down-regulated or induced/silenced under salt stress) was dynamically changeable under salt stress at different time intervals. All these results indicated that there was no established formula of gene expression patterns in deciphering the sophisticated mechanism of plant salinity tolerance, considering that plants undergo a series of dynamically physiological and metabolic pathways in sensing and response to salt stress for different tissues and during different stages of stress. A number of Trivially distributed file system (TDFs) up-regulated or induced under salt stress from leaves and roots were sequenced, and the sequences were blasted against the NCBI non-redundant protein database using translated nucleotide query (Blastx). The TDFs from K. virginica seedlings involved in sensing and response to salt stress can be classified at least into three groups according to their putative functions: (1) genes for re-establishing ionic homeostasis or preventing from damage (specially genes for transporter); (2) genes for resuming plant growth and development under salt stress, such as key enzymes involved in energy synthesis or hormone regulatory pathway; (3) genes for signal transduction and so on. The relationship of expression patterns of these TDFs with the molecular mechanism of salt tolerance in K. virginica was discussed.