Abstract: Abstract: Gymnosphaera podophylla is a famous relict tree fern with strong environmental adaptability. However, its adaptive mechanism is unclear. In this study, we sequenced root, stem, and leaf transcriptome of G. podophylla using PacBio and Illumina platform, and obtained 12879, 14185, and 16084 FL unigenes, respectively. Transcript quantification showed that these unigenes were related to drought resistance and biological stress, and were highly expressed. KEGG enrichment analysis showed that the up-regulated genes in the root, stem, and leaf were enriched to the secondary metabolic pathways such as "phenylpropane biosynthesis pathway" and "flavonoid biosynthetic pathway". Total 192 FL unigenes were annotated as the structural genes of 13 enzymes in the flavonoid biosynthesis pathway, including 112 DEGs, which suggested that the flavonoid biosynthesis pathway in G. podophylla was conserved and occurred organ-specific differential genes. It is the first report on comprehensively analysis of the full-length transcriptome of G. podophylla multi-organ and the structural genes of the flavonoid biosynthetic pathway, which provides abundant genetic resources for further investigation its environmental adaptation.