Various active components have been extracted from the root of Polygonum cuspidatum. However, the genetic basis for their activity is virtually unknown. In this study, 25600002 short reads (2.3 Gb) of P. cuspidatum root transcriptome were obtained via Illumina HiSeq 2000 sequencing. A total of 86418 unigenes were assembled de novo and annotated. Twelve, 18, 60 and 54 unigenes were respectively mapped to the mevalonic acid (MVA), methyl-D-erythritol 4-phosphate (MEP), shikimate and resveratrol biosynthesis pathways, suggesting that they are involved in the biosynthesis of pharmaceutically important anthraquinone and resveratrol. Eighteen potential UDP-glycosyltransferase unigenes were identified as the candidates most likely to be involved in the biosynthesis of glycosides of secondary metabolites. Identification of relevant genes could be important in eventually increasing the yields of the medicinally useful constituents of the P. cuspidatum root. From the previously published transcriptome data of 19 non-model plant taxa, 1127 shared orthologs were identified and characterized. This information will be very useful for future functional, phylogenetic and evolutionary studies of these plants.