Abstract: Ephedra sinica Stapf is not only an important medicinal plant rich in flavonoids and alkaloids， but also an important sandfixing plant in the desert environment. In this study， the transcriptome of E. sinica from SRA database in GenBank was further analyzed by bioinformatics method. 7 947 954 clean reads and 13 389 unigenes were acquired after de novo assembly; 10 481 annotations were acquired from Nr database， 4 533 from KOG database， 7 121 from GO database， 5 833 from KEGG database， 8 039 from SwissProt database after function annotation against five databases. We also discovered a series of unigenes which were associated with flavonoids biosynthesis by KEGG pathway analysis， which benefits the cloning of related genes and biosynthesis of related components in flavonoids pathway. This study could provide references for understanding the resistance mechanism of E. sinica and utilization of its medicinal value in the future studies.

Key words: Ephedra sinica Stapf, transcriptome, highthroughput sequencing, flavonoids