New drugs may be developed from secondary metabolites of medicinal plant metabolism. Identification of new metabolic pathways, unknown enzymes of vast unexplored medicinal plants will be a really very challenging area for future research. Information on underlying genes of unknown enzymes/metabolic pathways are hidden away in the dark matter of plant genomes. Genome sequencing and analysis by breakthrough sequencing technology like inexpensive NGS (Next-generation sequencing) technology may accelerate/fecilitate the gene identification. The emergence of this genomic research along with other omics research data including transcriptomic, metabolomics data may find out gene-metabolite linkage and discovery of new potential molecules. This review discusses the recent developments on medicinal plant genomic research and their importance in new drug discovery.