With at least 200 ethnic groups and 30.000 medicinal plants used in Jamu formulations, Indonesia is one of the largest natural drug dispensaries in the world. Ethnomedicine-directed bioprospecting has been used to accelerate drug discovery. Little is known about the coverage of ethnomedicinal studies in Indonesia. The quest to obtain drugs from plants also remains elusive. Nature-derived approved drugs worldwide have come mostly from drug-productive families that tend to be clustered in the phylogenetic tree, thus these families should be the basis of bioprospecting focus. We presented a review of ethnomedicinal research conducted across Indonesia and recommend strategic approaches to accelerate the translation of traditional knowledge into the clinic. We identified several plant species commonly used with similar or different purposes within different places, empirical pharmacological studies, regions that are understudied, and comparison with plants whose metabolites have been used for the development of approved medicine worldwide. Combination of ethnomedicinal knowledge with molecular phylogenetics,-omics, Bioactivity-guided bioprospecting, DNA barcoding, and Global Biodiversity Information Facility (GBIF) software will enable more efficient and environmentally friendly drug discovery process as well as commercial production. Altogether, this proposed method will be a game-changer in the exploration of the largely untapped chemical diversity of Indonesian flora.