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Platycladus orientalis (L.) is used extensively for afforestation and is a common medicinal ingredient. Because of its drought tolerance, P. orientalis is widely used for afforestation in arid and semi-arid areas. To better understand the mechanisms involved in drought-stress tolerance in this important tree, the transcriptome profiles of drought-treated P. orientalis seedlings were analyzed using Illumina technology, and differentially expressed genes (DEGs) between drought-treated and well-watered trees were identified. We performed transcriptome sequencing of P. orientalis roots using the Illumina 4000 paired-end sequencing technique. More than 53 million 151-bp paired-end clean reads were obtained from each of the cDNA libraries and biological replicates, and de novo assembly generated 148,392 unigenes with an average length of 927.77 bp. After removing contaminating sequences, we found that 29.9 % (34,845) of the unigenes exhibited significant similarity to known sequences in the GenBank non-redundant protein database. A total of 3930 unigenes were found to be significantly differentially expressed between drought-treated and well-watered trees. Among them, 881 (22.42 %) were up-regulated and 3049 (77.58 %) were down-regulated in roots. Several DEGs had known functions in categories related to the biosynthesis of secondary metabolites, phenylalanine metabolism, starch and sucrose metabolism, and arginine and proline metabolism. A total of 194 genes that were found to be differentially regulated in response to drought stress were categorized as transcription factors. The transcriptome profiles obtained provide a valuable resource for future research to understand the molecular adaptation of Cupressaceae plants under drought condition and facilitate the exploration of drought-tolerant candidate genes.