One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds. Genome wide high throughput technologies such as genomics, transcriptomics, proteomics and metabolomics can help reach that goal. Such technologies can produce a vast amount of data which desperately need bioinformatics and systems biology to process, manage, distribute and understand these data. By dealing with the “omics” data, bioinformatics and systems biology can also help improve the quality of traditional medicinal materials, develop new approaches for the classification and authentication of medicinal plants, identify new active compounds, and cultivate medicinal plant species that tolerate harsh environmental conditions. In this review, the application of bioinformatics and systems biology in medicinal plants is briefly introduced. One important purpose to investigate medicinal plants is to understand genes and enzymes that govern the biological metabolic process to produce bioactive compounds. Genome wide high throughput technologies such as genomics, transcriptomics, proteomics and metabolomics can help reach that goal. amount of data which desperately need bioinformatics and systems biology to process, manage, distribute and understand these data. By dealing with the “omics ” data, bioinformatics and systems biology can also help improve the quality of traditional medicinal materials, develop new approaches for the classification and authentication of medicinal plants, identifying new active compounds, and cultivate medicinal plant species that tolerate harsh environmental conditions. In this review, the application of bioinformatics and systems biology in medicinal plants is briefly introduced.