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Taxodium ’Zhongshanshan’ is an interspecies hybrid of Taxodium distichum and Taxodium mucronatum, and has been widely planted in southeastern China. It has great ecological and economic potential. However, the scant genomic resources in genus Taxodium have greatly hindered further exploration of its underlying salinity-tolerance mechanism. To understand the genetic basis of its salt tolerance, high throughput sequencing of mRNA (RNA-Seq) was used to analyze transcriptome changes of ’Zhongshanshan 405’ clone roots treated with NaCl stress. After de novo assembly, 70,312 unigenes were achieved, and 41,059 of them were annotated. 9038 differentially expressed genes (DEGs) were identified among the treatments, and 7959 DEGs were found between salt-stressed roots and control, with 489 up regulated and 570 down-regulated shared by all of the treatments. Genes related to transport, signal transductions as well as undescribed transcripts were among those DEGs in response to salt stress. Gene ontology classification analysis revealed that salt stress-related categories including ’oxidoreductase activity’, ’metal ion binding’, and ’membrane’ were highly enriched among these DEGs. Moreover, the gene expression pattern of 12 unigenes revealed by quantitative real-time polymerase chain reaction (qRT-PCR) confirmed the RNA-Seq data. Our study not only provided the large-scale assessment of transcriptome resources of Taxodium but also guidelines for probing the molecular mechanism underlying ’Zhongshanshan’ salt tolerance. (C) 2016 Elsevier Masson SAS. All rights reserved.