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Hordeum brevisubulatum is a valuable halophytic grass. To identify regulators and dissect the regulatory mechanisms for salt tolerance in H. brevisubulatum, we employed cDNA-AFLP technique to screen the differentially expressed fragments or genes in H. brevisubulatum seedling roots under salt stress, in which HbCIPK2 was identified to significantly respond to abiotic stresses, including NaCl. Constitutive over-expression of HbCIPK2 in Arabidopsis enhanced salt tolerance and rescued the salt sensitivity of sos2 knockouts, and over-expressing plants were found to have reduced shoot Na+ and increase K+ in the root, and improve the osmotic stress tolerance. HbCIPK2 from halophyte may function in different ways compared with CIPKs in glycophytes such as Arabidopsis, implying novel HbCIPK2-mediated salt signaling pathways or networks in halophyte H. brevisubulatum.