Alpine areas are hot spot of biodiversity and harbor high value medicinal plants. However, habitat destruction and anthropogenic disturbance have led many plant species to various levels of threat. Meconopsis aculeata Royle belonging to family Papaveraceae is one such alpine plant species with known medicinal properties. It is analgesic and febrifuge and has cooling potency. The plant is used in Tibetan medicine and used for the treatment of bones near the ribes. The flowers are used to treat asthma, body pain and fever. In the alpine areas of Uttarakhand the species has been found to have restricted distribution confined to specific habitats. M. aculeata has been reported to be endangered as per the IUCN red list and thus there is a need to make a population assessment of the species in the region. Thus, present study was conducted in areas of its occurrence representing the natural populations in Districts Chamoli and Rudraprayag. The sites were Valley of Flowers, Hemkund, Madhmaheshwar, Rudranath and Tungnath. The study revealed a substantial variation in frequency, density and IVI in the five sites. Highest Frequency was 47.22% in Tungnath and lowest 25.81% in Rudranath whereas maximum IVI 9.55 was recorded in Valley of Flowers and minimum 2.96 in Rudranath. Remaining three sites had IVI ranging from 3.72 to 4.05. Contrary to this, the highest density with 2.75 individuals/m2 was recorded in Madhmaheshwar followed by 2.00 individuals/m2 in Tungnath, 1.15 ind/m2 in Valley of Flowers and minimum 0.71 and 0.58 ind/m2 in Rudranath and Hemkund respectively. On overall assessment basis the species is critically endangered. Phytochemical constituents like terpenoids, tannins, alkaloid and phenols were determined in leaves from all the populations that also revealed considerable variations. The mature individuals of the species in the populations were in low number that further indicates need for devising conservation strategy for the species. © 2021, The Author(s), under exclusive license to Springer Nature Switzerland AG.