Thellungiella halophila is a salt-tolerant close relative of Arabidopsis thaliana. Significant mRNA similarity was confirmed by hybridization of T. halophila mRNA with the A. thaliana GeneChip ATH1. To establish a platform for future molecular comparison of the two species several physiological mechanisms, which may confer high salt tolerance to T. halophila, were investigated. Determination of ion content in shoots and roots of A. thaliana and T. halophila indicated different strategies of ion uptake and translocation from root to shoot in the two species. During salt stress T. halophila accumulated less sodium than A. thaliana. Tissue concentrations of sodium and potassium showed negative correlation in A. thaliana but not in T. halophila. Electrophysiological experiments proved high potassium/sodium selectivity of root plasma membrane channels in T. halophila. In particular, voltage-independent currents were more selective for potassium in T. halophila than in A. thaliana. Single cell sampling of T. halophila leaves during salt exposure revealed increased concentrations of sodium and decreased concentrations of potassium in epidermal cells suggesting that this cell type could function to ensure storage of sodium and exchange of potassium with the rest of leaf. Application of salt resulted in a sharp drop of transpiration in A. thaliana. By contrast, transpiration in T. halophila responded more slowly and was only slightly inhibited by salt treatment, thus maintaining high water uptake and ion transport.