To understand the molecular and cellular mechanisms underlying the salt response and to isolate differentially expressed genes, we constructed a forward subtractive cDNA library from Salsola ferganica treated with 600 mM NaCl for different lengths of time (0, 4, 8, 12, 16, 24, 36 h) using the suppression subtractive hybridization (SSH) technique. This SSH library contained approximately 2,200 positive clones, with the insert size ranging from 250 to 700 bp. Eighty clones were selected for further study based on results from reverse Northern blotting and sequencing and, these cDNAs are the first reported expressed sequence tags (ESTs) of Salsola ferganica listed in GenBank. Among these 80 differentially expressed genes, 32 are genes with known function that display a high homology (between 68 and 100% identity) to known sequences, 47 have an unknown function, showing no homology with known sequences, and one is a novel gene that does not match any previously reported genes. Five cDNA fragments, sf3d8, sf6d8, sf4a8, sf8d6, and sf6c7, were randomly chosen from the 80 differentially expressed genes for reverse transcription-PCR analysis. The expression of sf8d6 was entirely induced by salt stress and that of sf3d8, sf6d8, sf4a8, and sf6c7 was increased from a relatively lower level. The isolated ESTs reported here may enable us to find new genes involved in salt tolerance in Salsola ferganica. © 2010 Springer Science+Business Media B.V.