Here, we review CRISPR-based tools and briefly introduce their research histories, structural characteristics, working mechanisms, and derivative tools and discuss how they are being used in medicinal plant gene editing. The application of the CRISPR-Cas system to gene functional studies and metabolic networks regulation of medicinal plants is essential and meaningful, presenting a promising method for improving quality and breeding ideal germplasms in medicinal plants. Scientists are increasingly focusing on mining critical genes in metabolic pathways and finding novel synthetic methods for increasing the production of effective compounds. With the accumulation of studies on medicinal plants, more and more high-quality reference genome and efficient transformation systems of medicinal plants have been established, such as Salvia miltiorrhiza, Dendrobium officinale, Cannabis sativa and Opium poppy. Medicinal plants have been used for thousands of years, and bioactive natural compounds from medicinal plants play an important role in protecting health via the pharmaceutical and food industries, but they also represent important value in perfume, agrochemical, cosmetic industries. However, the application of this technology to medicinal plants has not been extensively explored because of their complex genetic backgrounds, inefficient genetic transformation system and regeneration system. Owing to its strong technical advantages, CRISPR-Cas system instantly became a major area of interest within the field of molecular biology and has been successfully applied to targeted gene editing in many model plants and crops. The CRISPR-Cas technology relies on the complementary pairing of guide RNA sequences with target DNA sequences to identify target sites, requiring only 20 nucleotide sequences to be artificially designed to target specific genes. In 2013, the third-generation clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene editing system was introduced, which corrected certain defects in the first- and second-generation gene editing systems based on the synthetic endonucleases zinc finger endonuclease (ZFN) and transcription activator-like effector nuclease (TALEN), such as the transfection inefficiency, design complexity and limitations on multiplexed mutations. Thus, it is preferred by most biologists. The targeted gene editing technology can precisely modify the locus information of a genome, achieve targeted gene deletion, insertion or replacement, and reduce impact on the receptor genome background. The traditional gene editing technology randomly integrates a target gene into a receptor genome, thus producing results with poor predictability and problems, such as gene silencing and unexpected variations. CRISPR-Cas is expected to revolutionize medicinal plant biotechnology in the near future. The aim is to provide a reference for the application of this technology to genome functional studies, synthetic biology, genetic improvement, and germplasm innovation of medicinal plants. Furthermore, we creatively put forward the development direction of CRISPR technology applied to medicinal plant gene editing. Here, we review the research history, structural characteristics, working mechanism and the latest derivatives of CRISPR-Cas technology, and discussed their application in medicinal plants for the first time. However, the application of CRISPR-Cas technology to medicinal plants is still in the early stages. An increasing number of plant species have been subjected to site-directed gene editing through this technology. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene editing technology has opened a new era of genome interrogation and genome engineering because of its ease operation and high efficiency.

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