Banebaghi is considered as a natural interspecific hybrid that can be used as rootstock for the genus of pistachio. In order to evaluate the effect of salinity stress on microelement concentration in as a Banebaghi natural hybrid, a factorial experiment was conducted based on completely randomized design with salinity levels (0, 60, 120 mM of salty sodium chloride, calcium chloride, magnesium chloride 3:2:1) and two growth types (mutica Type growth and pistachio Type growth) and height (height group lower than middle and height group more than middle) and three replications. According to the result, salinity decreased root Fe and shoot Mn concentration and increased Fe content of shoot. The highest shoot Fe content was observed in the mutica type growth with height group of more than the middle and the lowest Fe concentration of shoot in Pistachio type growth with height group of less than the middle. The maximum Cu concentration of shoot observed in type growth Pistachio with height group of less than the middle which increases of concentration was more evident than height group more than middle. Increasing salt concentration increased root Zn content in mutica growth type. The results of present study showed that microelements concentration in mutica type growth with height group of more than the middle and in Pistachio type growth with height group of less than the middle was more than the other treatments.