We have isolated the cDNA of Ca2+/H+ antiporter which was designated as Suaeda salsa cation exchanger 1 (SsCAX1) from the C-3 halophyte S. salsa L. To ascertain the location of SsCAX1 in the cell, a peptide-specific antibody to SsCAX1 was prepared, and Western blotting analysis showed that it reacted only with a 48.8-kDa protein from S. salsa vacuolar membrane. Furthermore, SsCAX1 could resume yeast vacuolar Ca2+ transport mutants growth in high Ca2+ concentration (200 mM) culture medium. Northern blotting analysis showed that SsCAX1 expression was mainly found in the leaves and stems and slightly in the roots of S. salsa seedlings. Moreover, SsCAX1 expression levels and the protein amounts were significantly upregulated by CaCl2 and NaCl treatment, respectively. In addition, the upregulation of the expression levels of V-H+-ATPase subunit c coordinated with the expression levels of the Ca2+/H+ antiporter under salinity. These results suggested that SsCAX1 from halophyte S. salsa might be a Ca2+ transporter at tonoplast and plays a key role in maintaining cytosolic Ca2+ homeostasis under saline condition.