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Iranian and Chinese traditional medicines recommended for health promotion and well-being. Chinese herbal drugs have been described by medieval Muslim medical scholars such as Tabari, Rhazes, Haly Abbas, Avicenna and Jurjani (1137 CE). Traditional Chinese and Iranian medicine play an important role in sustainable agriculture and food systems, it also offers a holistic approach to prevent diseases while making appropriate use of organic and herbal products especially growth by small-scale family farmers. Comparative genomics provides a method to unravel the relationship between genomes by describing conserved chromosomes or chromosomal regions between related species. There has been a significant increase is the number of sequences genomes of medicinal plant species. It is also clear that it is possible to use plant genome as a tool for improving breeding strategies. More researches are needed to introduce the genome research of medicinal plants, including genome sequencing, assembly, annotation, and functional genomics to set up the foundation for progress and development of natural medicines and also the appropriate selection of cultivars with good agricultural traits.