Ginkgo biloba is a well-known living gymnosperm fossil that has medicinal, biological, and economic value in the world. In this study, molecular characterization and bioinformatics analysis based on homology modeling were obtained by GbGSTs and GbCHS genes, which are crucial in the pathway of plant flavonoids, anthocyanins, and other significant secondary metabolites in plants. The results indicated that a 687 bp open reading frame (ORF) encoding a 228 amino acids protein with a determined molecular weight of around 25.786 kDa were found in the full-length cDNA of the GbGSTs gene sequence that was isolated from G. biloba. Whilst the full-length cDNA of the GbCHS gene sequence contained a 1176 bp (ORF) encoding a 391 amino acids protein with a predicted molecular weight of about 43.078 kDa. Additionally, phylogenetic analyses were carried out using the amino acid sequences of GbGSTs and GbCHS with other recognized plants that were obtained from NCBI. Multiple Sequence Alignment (MSAs) of chosen (30) amino acids with high identity and similarity using MEGA7 software, ProtParam software was used to the molecular weight and grand average of hydropathicity (GRAVY), and Protscale software was used to the hydrophilicity scales based on various. Finally, the molecular characterization and bioinformatics analysis of GbGSTs and GbCHS genes encoding key enzymes is the first step to fully understanding the regulatory mechanisms controlling flavonoid and anthocyanin biosynthesis in G. biloba. Keywords: Ginkgo, GbGSTs gene, GbCHS gene, Phylogenetic tree, flavonoid