Soil salinization is becoming a serious threat to crop yield all over the world. Nowadays, acquainting the specific molecular mechanisms underlying various abiotic stresses especially to salt stress should be of great importance. While the development of the high-throughout sequencing technology promoted the progress powerfully. The intricate perception, transduction and regulation mechanisms underlying salt stress are being illustrated more and more clearly. As a perennial halophytic plant, Kosteletzkya virginica is able to help us to understand the mechanisms more directly and effectively. We carried out the whole transcriptome analysis on young seedlings with or without salt treatment through high-throughout sequencing technology. The results revealed that the numbers of different expressed transcripts between control and different treatments are 4145 and 9134, respectively. The ORF prediction suggested that there were 94308 ORF out of the 103489 (91.10%) total transcripts. We also carried out further differential expression analysis through gene ontology (GO) classification, cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In a word, our transcriptome study on Kosteletzkya virginica would provide direct and effective references for researches on molecular mechanisms of salt-tolerance, extending our view of salt tolerance in plant further. Above all, the related report in this paper is the first about Kosteletzkya virginica.