The tropical forests of South and Southeast Asia hold the highest gliding squirrel diversity but our knowledge of species diversity, ecology and major threats is limited. The present study was undertaken in Arunachal Pradesh, Northeast India between June 2011 and March 2015 to address the paucity of data available on gliding squirrels. Based on field and literature surveys, 14 species of gliding squirrels were detected in the state of Arunachal Pradesh. However, species such as Biswamoyopterus biswasi, which is reported as endemic to Namdapha National Park, were not detected. The high gliding squirrel diversity in this region could be related to a diversity of forest types and its location between the Himalayas and the Indomalayan region. Encounter rates with four different species revealed that Petaurista petaurista was most frequently detected in Namdapha National Park. Major threats include hunting for traditional medicine, cultural purposes or bushmeat, and habitat loss due to forest degradation caused by shifting cultivation. In addition, more intensive studies on population, ecology and conservation status are needed in order to design species and site specific conservation action plans in this region which represents the highest diversity of gliding squirrels globally.