Medicinal plants have been used for therapeutic purposes for thousands of years. However, as the need for their greater diversity and quantity increases, new techniques are being used in the field of breeding, which include faster biotechnology and genetics processes to support these highly useful plants. Genetic diversity assessment is important for planning an effective breeding program for new and diverse medicinal plants. Thus, fast and efficient methods such as DNA microarrays, RNA sequencing, and DNA barcoding allows us to identify and detect genes to improve metabolic pathways. After the identification and classification of genes, we can use methods to target desired genes and thus increase the production of secondary metabolites or cause a change in their chemical profile. This is achieved by optimizing the culture medium of plant tissue cultures, elicitor additives, changing light intensity, cultivation in bioreactors, transformation processes with Agrobacterium sp., polyploid engineering and genome rearrangement methods such as ZFN, TALEN and CRISPR/Cas. Due to the endangered growth of medicinal plants in the natural environment, cryopreservation and encapsulation techniques into synthetic seeds are also important for maintaining the diversity of genetic material. The focus of this work is a review of methods presented above, which bring or will bring improvements of prized medicinal plants.