Salinity is a major abiotic stress which affects crop plants around the world, resulting in substantial loss of yield and millions of dollars of lost revenue. High levels of Na+ in shoot tissue have many adverse effects and, crucially, yield in cereals is commonly inversely proportional to the extent of shoot Na+ accumulation. We therefore need to identify genes, resistant plant cultivars and cellular processes that are involved in salinity tolerance, with the goal of introducing these factors into commercially available crops. Through the use of an Arabidopsis thaliana mapping population, we have identified a highly significant quantitative trait locus (QTL) linked to Na+ exclusion. Fine mapping of this QTL identified a protein kinase (AtCIPK16), related to AtSOS2, that was significantly up-regulated under salt stress. Greater Na+ exclusion was associated with significantly higher root expression of AtCIPK16, which is due to differences in the gene's promoter. Constitutive overexpression of the gene in Arabidopsis leads to plants with significant reduction in shoot Na+ and greater salinity tolerance. amiRNA knock-downs of AtCIPK16 in Arabidopsis show a negative correlation between the expression levels of the gene and the amount of shoot Na+. Transgenic barley lines overexpressing AtCIPK16 show increased salinity tolerance.