Physio-biochemical responses of pistachio varieties including Pistacia vera L. ‘Ghazvini’ (GH), P. vera ‘Ghermez-Pesteh’ (GP) and P. atlantica subsp. mutica (M) were assessed under salt stress to understand the common mechanisms of salt tolerance in two popular Pistacia species. In the experiment, half-sib seedlings of the varieties were subjected to high (100 mM) and severe (200 mM) levels of NaCl-induced salinity for 90 days. Growth, physiological, biochemical and ionic parameters in the roots and shoots of plants were measured in the experiment. Salinity markedly declined plant growth, and increased the number of necrotic leaves (NL) and leaf abscission. In terms of physiological responses, salinity reduced the relative water content (RWC), membrane stability index (MSI) and the concentrations of photosynthetic pigments, but increased carbohydrates and proline content in the leaves. MSI of the leaves was positively correlated with the concentrations of anthocyanins and carotenoids. Salinity increased sodium content in root and shoot tissues of the plants, and decreased potassium concentration and K/Na ratio. Among the rootstocks, GH had better performance on all parameters. Despite the high concentration of Na+ and low K/Na ratio in the shoots, the lowest number of NL was found in GH under both salinity levels. The results indicated that salt tolerance in GH was most likely related to compartmentation of Na+ ions. Finally, accumulation of osmolytes and sodium compartmentation were considered to be the most important mechanisms in the salt tolerance of pistachio rootstocks.