show Abstracthide Abstractwe have performed transcriptome sequencing of leaf, stem, and root of two pistachio cultivars (Pistacia vera L. Sarakhs and P. vera L. Ghazvini) under salinity and control conditions on one lane of Illumina Hiseq 2000 to produce a robust pooled transcriptome assembly of P. vera. Our study, as the first report on the transcriptome sequencing of pistachio, will not only provide plenty of informative data, but also paves the way for functional and comparative genomic studies on this major tree and other woody species to decipher the potential abiotic stress response mechanisms.