Abstract: Panax quinquefolium is one of the most common medicinal plants worldwide. Ginsenosides are the major pharmaceutical components in P. quinquefolium. The biosynthesis of ginsenosides in different tissues of P. quinquefolium remained largely unknown. In the current study, an integrative method of transcriptome and metabolome analysis was used to elucidate the ginsenosides biosynthesis pathways in different tissues of P. quinquefolium. Herein, 22 ginsenosides in roots, leaves, and flower buds showed uneven distribution patterns. A comprehensive P. quinquefolium transcriptome was generated through single molecular real-time (SMRT) and second-generation sequencing (NGS) technologies, which revealed the ginsenoside pathway genes and UDP-glycosyltransferases (UGT) family genes explicitly expressed in roots, leaves, and flower buds. The weighted gene co-expression network analysis (WGCNA) of ginsenoside biosynthesis genes, UGT genes and ginsenoside contents indicated that three UGT genes were positively correlated to pseudoginsenoside F11, notoginsenoside R1, notoginsenoside R2 and pseudoginsenoside RT5. These results provide insights into ginsenoside biosynthesis in different tissues of P. quinquefolium.