Setting priority species for conservation planning in a large and biodiverse country such as Indonesia is crucial. At least 80% of the medicinal plant species in South East Asia can be found in Indonesia, whether they are native or introduced. However, their conservation is currently ineffective due to limited human and financial resources. By examining factors such as species' occurrence status, rarity and part of the plant harvested, the various Indonesian medicinal plant species can be prioritised for conservation planning. In this study, various threatened plant species have been included in the priority list as well as those listed in related legislation. Some 233 species within 161 genera and 71 families are recommended for prioritisation. An inventory of these priority species was produced presenting compiled data including vernacular names, plant habit, harvested plant part, uses, distribution, whether it is conserved ex situ, and their DNA barcoding. Significantly 41.20% of priority species have no information on their current conservation status in either in situ or ex situ national or international genebanks.