the stem of Dendrobium huoshanense c.Z. tang and S.J. cheng was widely used as a medicinal herb in health care products due to its broad pharmacological activities. However, the molecular regulation mechanism of stem development and biosynthetic pathways of important bioactive substances are still unclear in D. huoshanense. in this study, the bioactive compounds in leaves, stems and roots, and the identification of candidate genes involved in stem formation and biosynthesis of active compounds via transcriptome sequence were analyzed. The accumulation of total polysaccharides and flavonoids were varied significantly in different tissues. A comparative transcriptomic analysis revealed several differentially expressed genes (DEGs) involved in polysaccharides biosynthesis (103 genes), including fructose and mannose related genes (29 genes) and glycosyltransferase genes (74 genes), and flavonoids biosynthesis (15 genes). Some candidate genes that participated in photoperiod regulation (27 genes), starch and sucrose metabolism (46 genes), and hormone-induced activation of signaling pathways (38 genes) may be involved in stem formation. In sum, this study provides a foundation for investigating the molecular processes in the biosynthesis of active compounds and stem development. the transcriptome data presented here provides an important resource for the future studies of the molecular genetics and functional genomics in D. huoshanense and optimized control of the active compounds produced by D. huoshanense.Dendrobium huoshanense C.Z. Tang and S.J. Cheng is an edible and medicinal plant, and has been utilized as a tonic in Traditional Chinese Medicine for centuries 1 . Specifically, it is used for boosting immunity, slowing aging, and possesses anti-tumor properties 2,3 . At present, increased demands and over-exploration caused reduced yield of wild resource and the damage of D. huoshanense habitats. Although artificial cultivation is an efficient way to protect natural resources and develop a sustainable medicinal supply, it was still faced an important issue to ensure and improve the quality and yield of D. huoshanense under artificial conditions. Understanding the regulation mechanism of quality and production of D. huoshanense has huge commercial and health value.At present, several ingredients from D. huoshanense have been identified as therapeutic active components, such as polysaccharides 4,5 , flavonoids 6,7 , alkaloids 8,9 . Modern pharmacological researches have confirmed that polysaccharides can activate immune cells, modulate the immune responses in the intestines, spleen, and liver, and inhibit cell proliferation in tumors [10][11][12][13] . Alkaloids possessed the functions of anti-inflammatory, anti-diabetic effect and anticancer activity 14,15 . Flavonoids also possesses biological functions including anti-oxidant, anti-cancer, anti-aging, cardiovascular protection, and building of immunity [16][17][18][19] . The key genes associated with polysaccharides and alkaloids biosynthesis have been identified,...