A new discipline, herbgenomics, has emerged, which provides an effective platform to support the chemical and biological analyses of traditional medicines. Here, we report the whole genome sequence of Panax ginseng-the king of herbs-as well as its transcriptomes, metabolites and rhizophere metagenomics in order to help the analysis of ginsenosides biosynthesis and help the cultivation improvement. The 3.5 Gb nucleotide sequence contains more than 60% repeats and encodes 42 006 predicted genes, encompassing 488 cytochrome P450s, 2556 transcription factors, and 3745 transporter genes. Twenty-two transcriptome datasets and mass spectrometry images of ginseng roots were adopted to precisely quantify the functional genes. Thirty-one genes were identified to be involved in the mevalonic acid pathway. A total of 225 UDP-glycosyltransferase (UGTs) were identified, and these UGTs accounted for one of the largest gene families in ginseng. Tandem repeats contributed to the duplication and divergence of UGTs. Molecular modeling of UGTs in the 71, 74, and 94 families revealed a regiospecific conserved motif located at the N-terminus. Molecular docking predicted that this motif captured ginsenoside precursors. Metagenomics analysis revealed that bacterial diversity decreased, whereas fungal diversity increased, in the rhizosphere soils of adult ginseng plants at the root growth stage under different ages. Few microbial community, such as Luteolibacter, Cytophagaceae, Luteibacter, Sphingomonas, Sphingomonadaceae, and Zygomycota, were observed; the relative abundance of microorganisms, namely, Brevundimonas, Enterobacteriaceae, Pandoraea, Cantharellales, Dendryphion, Fusarium, and Chytridiomycota, increased in the soils of adult ginseng plants compared with those in the soils of 2-year-old seedlings. These work are expected to contribute to ginseng breeding, cultivation, and synthesis biology.