Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau and adjacent regions, is an important ornamental, medicinal and aromatic herb. In this study, a comprehensive transcriptome of 18 libraries from six organs namely, roots, stems, leaves, sepals, flowers and seeds of D. tanguticum were generated. More than 100 Gb of sequence data were obtained and assembled de novo into 187,447 transcripts, including 151,463 unigenes, among which the six organs shared 17.7% (26,841). In addition, all unigenes were assigned to 362 pathways, in which 'biosynthesis of secondary metabolites' is the second enriched pathway. Furthermore, rosmarinic acid (RA) is one of the multifunctional phenolic bioactive compounds produced in some Lamiaceae species. The six organs of D. tanguticum were confirmed to produce RA. A total of 22 predicted biosynthetic genes related to RA from the transcriptome were further isolated. Two of these genes were identified as candidates by evaluating the correlation coefficient between the RA contents and the expression of the predicted biosynthetic genes in the six organs. The new sequence information will improve the knowledge of D. tanguticum, as well as provide a reference tool for future studies of biosynthetic genes related to RA in this species.Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau (QTP) and adjacent regions, is an important ornamental, medicinal and aromatic herb. This plant is one of the important traditional Tibetan medicines which have been used by locals for a long time. However, no study has been reported on D. tanguticum because of the plant's limited distribution. The high-altitude QTP region has unique climate factors, including low oxygen levels, intense ultraviolet light, and large temperature difference between day and night, as well as prolonged daytime during the short growing seasons, which usually commences on April and ends in October for D. tanguticum. All of these harsh factors may be beneficial for the biosynthesis of protective secondary metabolites in D. tanguticum.Rosmarinic acid (RA) is a multifunctional phenolic bioactive compound that possesses astringent, antimutagen, antibacterial, antiviral, antifungal, anti-inflammatory and anti-oxidative activities [1][2][3][4][5][6] . An increasing number of plant sources have been screened for RA content 7-9 , and biotechnological and metabolic engineering approaches for RA production have been studied in previous reports [10][11][12][13][14][15] . However, plant sources have remained insufficient in meeting the rising demand of RA in recent years.Previous literature reported that the amino acids, L-phenylalanine and L-tyrosine, are the two precursors of the RA biosynthetic pathway in Coleus blumei, a Lamiaceae species 16 . In the phenylalanine-derived pathway of RA biosynthesis, phenylalanine ammonia-lyase (PAL) catalyses the oxidative desamination of phenylalanine, forming t-cinnamic acid, and cinnamic acid; 4-hydroxylase (C4H) introduces the par...