Since the completion of the Human Genome Project in 2000, the science of genomics rapidly developed. The application of genomics in medicinal plant research has become popular. In this study, we retrieved international research essays on medicinal plant genomics from 2000 to 2016 from the SCIE bibliographic database and performed data mining using the analysis platform CiteSpace and the analysis tool HistCite. The analysis revealed that studies conducted in China, India and the United States accounted for 29.3%, 19.2% and 10.8% of the total studies, respectively. The Chinese Academy of Medical Sciences, the Chinese Academy of Sciences, and Kyung Hee University as the main research institutions, accounted for 6.1%, 5.1% and 1.5% of the total studies, respectively. Chinese scholar Shilin Chen has played an important role in this research area, putting forward a new discipline, called herbgenomics. Future forecasting analysis revealed that China will continue to be the leading country in medicinal plant genomics, Cameroon and Vienna would engage in this research, and genomics of medicinal plants will be more closely integrated with multi-omics technologies, such as metabolomics, transcriptomics, etc. In addition, gene editing technology may provide new approaches into genomic studies of medicinal plants.