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Background  Human beings use plants for a multitude of purposes of which a prominent one across the globe is for their medicinal values. Medicinal plants serve as one of the major sources of income for high altitude inhabitants in the Himalaya, particularly in countries like Nepal, and Bhutan. People here harvest huge volumes of medicinal plants indiscriminately, risking their sustainability. This paper attempts to identify some of the priority medicinal plant species harvested in the wild and assess their ecological status for their judicious utilization, and to help provide policy guidance for possible domestication and support strategic conservation frameworks.    Results  Out of the 16 priority species identified by the expert group, collectors’ perception on ecological status of the priority species differed from survey findings.  Chrysosplenium nudicaule  (clumps) ranked as most threatened species followed by  Corydalis dubia , and  Meconopsis simplicifolia .  Onosma hookeri, Corydalis crispa and Delphinium glaciale  were some of the species ranked as threatened species followed by  Halenia elliptica  (not in priority list). Percent relative abundance showed irregular pattern of species distribution. High species evenness was recorded among  Nardostachys grandiflora ,  Chrysosplenium nudicaule ,  Saussurea gossypiphora  and Aconitum orochryseum with average species density of 8 plant m −2 .  Rhodiola crenulata , and  Dactylorhiza hatagirea  followed by  Meconopsis horridula  and  Meconopsis simplicifolia  were ranked as most threatened species with average species density of 0.4, 0.4, 5.6 and 6.0 plant m −2 , respectively. The most abundant (common) species was  Onosma hookeri  (plant m −2 ). Species composition and density also differed with vegetation, altitude, slope and its aspects.    Conclusion  Priority species identified by expert group were found vulnerable and patchy in distribution. Survey results and collectors’ perceptions tally to an extent. Some of the species ( Dactylorhiza hatagirea, Rhodiola crenulata, Meconopsis simplicifolia and Meconopsis horridula ) were critically low in plant density with less than a plant per m 2  while  Delphinium glaciale, Fritillaria delavayi and Aconitum orochryseum  were confined to narrow altitude range. Collectors were aware that most species identified in priority list are threatened and existing harvesting plan are hardly implemented as it is not pragmatic. Moreover, major chunk of medicinal plants harvested remain unaccounted as illegal harvest and marketing seemed to occur across the borders. Policing and monitoring would continue to be a challenge given the rugged terrain and harsh climate. In-depth study and further monitoring of low density species is suggested to ensure its sustainability through long term strategy development.    Electronic supplementary material  The online version of this article (doi:10.1186/s12898-016-0100-1) contains supplementary material, which is available to authorized users.

Ecological status of high altitude medicinal plants and their sustainability: Lingshi, Bhutan