Abstract: Gymnosphaera podophylla Dalla Torre & Sarnth. is a famous relict tree fern with strong environmental adaptability. However, the mechanisms underlying its adaptability remain unclear. In this study, the PacBio and Illumina platforms were used to sequence the root, rachis, and pinna transcriptomes of G. podophylla, resulting in the generation of 12 879, 14 185, and 16 084 full-length unigenes, respectively. Transcript quantification showed that these unigenes were related to drought resistance and biological stress and were highly expressed. KEGG enrichment analysis indicated that the up-regulated genes in the roots, rachis, and pinna were enriched in the "phenylpropane biosynthesis pathway", while the up-regulated genes in the roots and rachis were enriched in the "flavonoid biosynthetic pathway". A total of 192 full-length unigenes were annotated as structural genes involving 13 enzymes in the flavonoid biosynthesis pathway, including 112 differentially expressed genes (DEGs), suggesting that the flavonoid biosynthesis pathway was conserved in G. podophylla, with organ-specific DEGs. This research is the first to perform a comprehensive analysis of the full-length transcriptome across multiple organs in G. podophylla and to investigate the structural genes of the flavonoid biosynthetic pathway. This study provides an abundance of genetic resources for further examination of environmental adaptation in this species.