Abstract Plants use different strategies in response to environmental stress. Unsaturated fatty acids (UFAs) protect the plant against environmental stresses, especially temperature stresses, by regulating the fluidity of the cell membrane and also by scavenging reactive oxygen species (ROS) compounds. In this study, the expression changes of (Fatty Acid Desaturases) FAD 2, 3 and 4 genes as well as fatty acid profile in two species Pistacia khinjuk and Pistacia atlantica were studied in response to different climatic conditions. The results show that the highest content of polyunsaturated fatty acids (PUFAs) is related to P. khinjuk species in Anjirk (AJ) region. Also, the highest content of monounsaturated fatty acids (MUFAs) can be seen in the same region in P. atlantica species. Comparing the two species, it can be observed that P. atlantica relatively contains more unsaturated fatty acids. The lowest expression of desaturase genes in the studied samples was in the Jebalbarez (JE) region. These results prove that both studied species changed the expression of desaturase genes in response to stress and finally the nutritional quality of the plant has been affected.