Cycas pectinata Buch.-Ham. is an ancient gymnosperm that is now confined to pockets of habitats in the Indian subcontinent but was once widely distributed. Its decline is attributable to habitat loss, and has reached the point where C. pectinata is listed as ‘Vulnerable’ in the IUCN Red List. C. pectinata is the only species of Cycas found in Bhutan, and in this biodiversity-rich area it is present as a relic of great scientific and conservation value because of its rarity and long evolutionary history. Although it is well known in India, it has not been studied in detail in Bhutan. This study assessed populations and threats to C. pectinata in two places in Bhutan. Field visits were made to document the distribution, habitats, and associated threats to the populations. Plants were observed growing in steep rugged terrain in the open Chir Pine forest. Populations are significantly threatened due to human activities such as habitat destruction and over collection as ornamental plant. Possible expansion of populations is naturally threatened by low seed production and by predators.