Long non-coding RNAs (lncRNAs) play crucial roles in regulating gene expression in response to plant stresses. Given the importance regulatory roles of lncRNAs, providing methods for predicting the function of these molecules, especially in non-model plants, is strongly demanded by researchers. Here, we constructed a reference sequence for lncRNAs in P. vera (Pistacia vera L.) with 53220 transcripts. In total, we identified 1909 and 2802 salt responsive lncRNAs in Ghazvini, a salt tolerant cultivar, after 6 and 24 h salt treatment, respectively and 1820 lncRNAs in Sarakhs, a salt sensitive cultivar, after 6 h salt treatment. Functional analysis of these lncRNAs by several hybrid methods, revealed that salt responsive NAT-related lncRNAs associated with transcription factors, CERK1, LEA, Laccase genes and several genes involved in the hormone signaling pathways. Moreover, gene ontology (GO) enrichment analysis of salt responsive target genes related to top five selected lncRNAs showed their involvement in the regulation of ATPase, cation transporter, kinase and UDP-glycosyltransferases genes. Quantitative real-time PCR (qRT-PCR) experiment results of lncRNAs, pre-miRNAs and mature miRNAs were in accordance with our RNA-seq analysis. In the present study, a comparative analysis of differentially expressed lncRNAs and microRNA precursors between salt tolerant and sensitive pistachio cultivars provides valuable knowledge on gene expression regulation under salt stress condition. Pistacia belongs to Anacardiaceae family and contains 13 or more species, which among them pistachio (Pistacia vera L.) is the only cultivated and economically important species that is called as the 'green gold tree'. The other species are used mainly as a rootstock for pistachio cultivation 1,2. Like many other fruit trees, P. vera is hard to root and thus requires a rootstock for vegetative propagation 3. Pistachio is a deciduous (2n = 30), wind-pollinated tree species 4,5. Studies indicate that pistachio probably originated in the Middle East 6-8. It has a long history of cultivation (3000-4000 years) in Iran 9. In 2017, Iran has been ranked first in area harvested (429535 ha) and production quantity (574987 tons) of pistachio among United States, Turkey, and Syria as biggest pistachio producer countries 10. According to the number of pistachio genotypes, Iran is one of the rich countries in the world 7,8,11. In addition to fruit, other parts of plant, including leaf, flower and resins, have pharmacological properties 12,13. Salinity is major and ever-increasing problem in arid and semi-arid regions that affect plant production and growth throughout the world 14. The cultivated areas of pistachio in Iran are often in arid and semi-arid regions that the most important problem for economic crop production in these areas is high concentration of ions