Rattans, the climbing palms, are one of the most important non-wood forest produce supporting the livelihood of many forest dwelling communities in India. However, extensive harvest, loss of habitat and poor regeneration has resulted in dwindling of rattan populations necessitating an urgent need to conserve the existing rattan genetic resources. In this study, using GIS tools, an attempt has been made to develop species richness maps of rattans in the North-Eastern Himalaya, a megadiversity region in India. At least four sites of extremely high species richness were identified that could be prioritized for in situ conservation. Further, using molecular tools, genetic variability was assessed in six populations of an economically important rattan, Calamus flagellum. The population that was least disturbed or harvested maintained comparatively higher levels of genetic diversity than those that were disturbed. The study, perhaps the first in the region, emphasizes the need for developing strategies for the long-term conservation of rattans in the North-Eastern Himalaya.