Any deviation from the optimal conditions for the living organisms means stress. Low temperature is one of the major stresses that negatively affects the potential production of agricultural crops. Cell membrane is the first live part of the cell that is exposed to the environmental stresses. The response of plants to low temperatures depends on the duration and the intensity of the stress. To cope with adverse environmental conditions, plants set up special molecular mechanisms. Since adsorption of water and nutrients are the root’s function, so the root adaptation process is very important in response to low temperatures. Increasing activity of plasma membrane ATPase proton pump after cold adaptation is a mechanism that plants use against damages caused by low temperature stress. Improvement of mineral nutritional status of plants is essential for their survival and high yield under conditions of environmental stresses. Zinc is one of the elements that play a very important role in protecting plants against low temperature stress. One of the functions of zinc in the cell is maintaining the integrity and permeation control of the biological membranes. Although zinc sulfate is the most common source of zinc for plants, in recent years, the use of natural organic chelates, including zinc-amino acid complexes, has been welcomed by farmers. In this research, the effect of chilling stress (4 ° C for 6 hours and 18 hours) and freezing stress (-4 ° C for 6 hours) on zinc uptake mechanisms and activity of ATPase proton pump in two wheat cultivars under zinc deficiency and the effect of zinc and presence of lysine on the stress responses of the two wheat cultivars were investigated. The experiments were conducted in a completely randomized design with a factorial arrangement with three replications. The results showed that the duration and intensity of the low temperature stress affected, differently, the ATPase proton pump activity of the roots plasma membrane and the active and passive uptake of Zn. Short-term chilling stress and freezing stress reduced the plasma membrane ATPase proton pump activity and the total uptake of Zn by root, mainly due to reduction of the active uptake. This negative effect was lessen by the presence of Zn. With the increase in the duration of cold stress and probably due to plant acclimation, the activity of H + -ATPase in the plasma membrane and uptake of the roots increased. In the recovery period, after the stress treatments, the activity of the H + -ATPase pump, proton traort and root uptake improved. Zinc treatment in presence and absence of lysine in compare with absence of zinc in all temperature treatments increased the activity of the H + -ATPase pump and increased the traort of proton and zinc uptake by roots. Although the activity of the H + -ATPase pump in the presence of lysine with zinc was lower than the absence of lysine, the lysine + zinc also increased the amount of proton traort and root uptake above the zinc treatment alone. Keywords : Chilling stress- Freezing stress- Zinc- Active and passive uptake- H + -ATPase Pump- Proton traort