| Summary: | A new <i>Populus</i> variety with a strong salt tolerance was obtained from cross breeding <i>P. talassica</i> as the female parent and <i>P. euphratica</i> as the male parent. In order to elucidate the molecular mechanism and find out the major differentially expressed genes of salt tolerance of <i>P. talassica × P. euphratica</i>, after being subjected to salt stress, at 0, 200, and 400 mmol/L NaCl, the root, stem, and leaf transcriptomes (denoted as R0, S0, and L0; R200, S200, and L200; and R400, S400, and L400, respectively) of <i>P. talassica</i> × <i>P. euphratica</i> were sequenced. In total, 41,617 differentially expressed genes (DEGs) were identified in all the comparison groups with 21,603 differentially upregulated genes and 20,014 differentially downregulated genes. Gene Ontology analysis showed that DEGs were significantly enriched in biological processes that may be involved in salt stress, such as ‘cell communication’, ‘ion transport’, ‘signaling’, and signal ‘transmission’. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEGs were mainly enriched in pathways of ‘plant–pathogen interaction’, ‘carbon metabolism’, and ‘plant hormone signal transmission’. The pathways and related gene information formed a basis for future research on the mechanisms of salt stress, the development of molecular markers, and the cloning of key genes in <i>P. talassica</i> × <i>P. euphratica</i>.
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