Isatis indigoticaIsatis Indigotica Fortune belongs to the genus Isatis L. in the Brassicaceae family, and widely grown in China. It produces indicanIndican and isatan BIsatan B as the source of indigoIndigo dye, while terpenoidsTerpenoids, lignans and indole alkaloidsAlkaloids as effective metabolites against bacteria, viruses, and fungi. There is a high demand for plant secondary metabolitesSecondary metabolite, but the production is in shortage. Although there is no any comprehensive conventional breedingConventional breeding study on I. indigotica, geneticGenetic engineeringGenetic engineering and tissue cultureTissue culture methods are promising. Biotechnological methods such as somatic hybridizationSomatic hybridization and protoplast fusion methods enabled hybridHybrids plants, which are impossible in conventional cross. Transgenik pest resistant tetraploid I. indigotica plants could be produced efficiently through Agrobacterium tumefaciens mediated transformation. The cloned tetraploid I. indigotica plants with geneticGenetic engineeringGenetic engineering could be used in conventional breedingConventional breeding studies as parental lines. The concentrations of effective secondary compounds such as indigoIndigo, indurubin, amino acids, anti-endotoxic and antiviral compounds were higher due to the larger organs of tetraploids, which obtained in tissue cultureTissue culture and displayed higher resistance to insects, cold, drought and diseases than their diploids. However, the demand for tetraploid I. indigotica as a medicinal plantMedicinal plants has increased, but the demand cannot be met sufficiently. For future perspective, the molecular and conventional breedingConventional breeding methods might lead to improved varietiesVarieties and increased production of the effective metabolites, which can be used in alternative medicine. Considering the characteristics of I. indigotica, the expansion and development of its production around the world will turn into a great health benefit for community.