Herbal medicines, originating from plants or fungi, have been utilized for over 5000 years and remain a vital and indispensable component of contemporary healthcare, helping to reduce the impact of diseases on human health.(p1) Traditional herbal medicine remains a vital aspect of many cultures worldwide, contributing to modern pharmaceutical discoveries and alternative treatments.(p2) However, as demand for herbal products grows, concerns about overharvesting, habitat destruction caused by anthropogenic factors, and the inconsistent quality of herbal medicines have highlighted the need for more sustainable approaches in herbal resource management.(p3) To address these issues, modern genetic tools and omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, are now playing an increasingly pivotal role in optimizing herbal resources. Omics research into the genetic foundations of traditional herbs plays a significant role in uncovering their biological mechanisms, ensuring medicinal quality, advancing herbal synthetic biology, protecting natural herb resources, and enhancing drug safety. As a result, these technological advancements are expected to significantly drive the ongoing development and improvement of human health.(p4) Overall, the integration of genetic insights into herbal resource management not only optimizes the therapeutic potential of medicinal plants but also promotes sustainable practices in plant cultivation and conservation. This evolution in research has the potential to revolutionize the future of herbal medicine, providing a more reliable, scientifically supported foundation for the continued use of plants in modern healthcare. The intersection of genomics and traditional medicine has opened transformative possibilities for understanding and utilizing medicinal plants. Herbgenomics is an emerging platform that unravels medicinal plant biology using multiple-omics approaches and its potential applications. It plays a vital role in integrating ethnobotanical knowledge with modern molecular biology, thereby enhancing the discovery and development of plant-based therapeutics.(p5) The current review outlines the integration of herbgenomics with multiple-omics tools and their key applications in research, drug development, breeding, conservation, and functional analysis for sustainable optimization of medicinal plant resources.

Plant-derived natural products such as artemisinin, aspirin, atropine, ephedrine, morphine, podophyllotoxin, vinblastine, and taxol remain central to modern medicine, yet their large-scale use is often limited by inconsistent metabolite levels, variable raw material quality, and restricted availability. Securing a sustainable supply therefore depends on accurate species identification, the development of genetically improved cultivars, appropriate cultivation practices, and adaptation to diverse environments. A persistent challenge, however, is the lack of stable, high-yielding varieties that can reliably support pharmaceutical production. In recent years, the rise of herbgenomics, integrating genomic and multi-omics technologies with traditional herbal research, has created new opportunities to address these issues by clarifying species identity and unraveling the biosynthetic pathways that underlie alkaloids, flavonoids, terpenoids, and other pharmacologically active metabolites (Figure 1). High-quality genome assemblies have enabled comparative analyses that reveal phylogenetic diversity, evolutionary dynamics, and pathway conservation. Advances in sequencing and computational biology now allow detailed examination of biological processes at the genetic, transcriptional, and metabolic levels, with research moving steadily from single-omics to more comprehensive multi-omics approaches. Herbgenomic research has increasingly emphasized identifying DNA and chemical markers for species classification,(p6),(p7) mapping functional genes associated with agronomic traits,(p8),(p9) characterizing biosynthetic pathways of bioactive compounds,(p10),(p11) and dissecting the molecular mechanisms of stress responses.(p12),(p13),(p14),(p15) These developments provide a stronger foundation for synthetic biology and open new directions for molecular breeding. Reverse and forward genetics have been essential for identifying genes associated with specialized metabolites and quality traits, with Artemisia annua serving as a model species. Even so, the application of genomic discoveries in breeding remains slow, complicated by genome complexity, polyploidy, and the need for functional validation. Genome-editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) hold considerable promise for fine-tuning biosynthetic pathways, but regulatory constraints, technical difficulties, and concerns over public acceptance continue to limit their adoption. Taken together, herbgenomics is reshaping approaches to the cultivation, conservation, and pharmaceutical use of medicinal plants. Progress in the field will rely on the expansion of high-quality reference genomes, improved annotation of biosynthetic pathways, robust validation of candidate gene functions, and transparent regulatory frameworks that support the responsible application of genomic and genome-editing technologies.