Among the different species of Pistacia genus, P. atlantica is more distributed in cold area than P. khinjuk. In this study, in order to illustrate the physiological mechanisms of cold tolerance under acclimation phenomenon, two experiments were established. First experiment was conducted to induction of acclimation on seedlings at two stages and each stage was done for two weeks with different photoperiods. Then chlorophyll and florescence's chlorophyll was measured. For second experiment, leaves and stems of seedlings were exposed to three levels of temperature, +4°C (control), -20°C in one hour and -20°C in two hours. For this purpose, we measure relative water content (RWC) and electrolyte leakage (EL). Results of first experiment showed that 44% electron transport rate and 46% photochemical quenching was significantly reduced. This reduction in P. atlantica was grater by 30% compared to P. khinjuk. Second experiment results revealed that leaf RWC and EL increased during cold acclimation to be 8 and 11%, respectively. In addition, stem EL increased only in P. khinjuk (44%). In fact, P. atlantica due to decreasing of RWC during acclimation was able to maintain the photosystem efficiency and showed more resistance to cold stress. According to our findings, we can identify cold-resistant species or genotypes by measuring the florescence's chlorophyll.