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Ziziphus nummularia (Burm. f.) Wight & Arn., a perennial shrub that thrives in the arid regions, is naturally tolerant to drought. However, there are limited studies on the genomics of drought tolerance in Ziziphus sp. In this study, RNA-sequencing of one month old seedlings treated with PEG 6000 was performed using Roche GS-FLX454 Titanium pyrosequencing. A total of 367,176 raw sequence reads were generated, and upon adapter trimming and quality filtration 351,872 reads were assembled de novo into 32,739 unigenes. Further characterization of the unigenes indicated that 73.25% had significant hits in the protein database. Kyoto encyclopedia of genes and genomes database (KEGG) identified 113 metabolic pathways from the obtained unigenes. A large number of drought-responsive genes were obtained and among them differential gene expression of 16 highly induced genes was validated by qRT-PCR analysis. To develop genic-markers, 3,425 simple sequence repeats (SSRs) were identified in 2,813 unigene sequences. The data generated shall serve as an important reservoir for the identification and characterization of drought stress responsive genes for development of drought tolerant crops.