Dioscorea composita is an important medical and energy plant used for extracting different biological active substance and producing bioethanol.Flavonoids are significant material to the plants because they protect the plants from UV and the bacteria.However the male and female Dioscorea composita has a big difference in content of flavonoids.Using Illumina deep sequencing,62,341 unigenes were obtained by assembling in its transcriptome and 28,026 unigenes were annotated.8,022 unigenes were mapped to 244 specific pathways and 531 unigenes were identified to involve in 24 second metabolic pathways.The result of Real-time PCR about five related transcripts shows that the expression of core enzymes in flavonoids biosynthesis is This research not only help us know more about the genome of Dioscorea composita,but also benefit the follow study of it.