SRP140800 PRJNA449144 Hippophae rhamnoides subsp. sinensis Transcriptome or Gene expression Illumina HiSeq high-throughput sequencing technology was applied to get the transcriptome from leaves of female and male plants leaves in Hippophae rhamnoides L. subsp. sinensis. Via sequencing, 48.31 Gb effective data was obtained with an average error rate of 0.015%. After de novo assembly by the software of Trinity, a total of 320876 unigenes and 187362 transcripts were generated, accounting for maximum length of 17291 bp, the average length of 588 bp and 808 bp respectively. Using Blastx against the public databases, 104926 unigene were annotated in at least one databases. In addition, 33248 potential SSR loci were detected throughout the transcriptomic data. 92970 genes showed differences in expression levels between the transcriptome of female and male plants leaves of Hippophae rhamnoides L. subsp. sinensis. This work provides basic data for the gene cloning and gene mining, as well as to investigate the sex-determining mechanism of dioecious Hippophae rhamnoides L. subsp. sinensis. Hippophae rhamnoides subsp. sinensis