The Indian Pangolin Manis crassicaudata, is an ‘Endangered’ mammal species native to Pakistan but facing a risk of extinction due to hunting pressure for its scales used in trade. The current study investigated habitat preference of this unique species in the Margalla Hills National Park, Islamabad, from September 2011 to August 2012. Three habitat types, viz, human vicinity area, agricultural land, and wild/natural area, were searched for recording signs of Indian Pangolin. Data on habitat preference was collected from direct and indirect signs of the species by monitoring 85 line transects, each measuring 500m in length and 50m in width, in 17 different sampling sites. A total of 323 signs of Indian Pangolin were recorded including 299 burrows, 10 live sightings, and 14 scats of the species. The maximum number of signs were recorded in wild or unmodified natural area (55.1%), followed by those in vicinity to human use area (20.12%), while the least (24.76%) were found in agricultural area. Statistical comparison using one-way analysis of variance of pangolin field signs, among three different types of habitats studied, differed significantly (df= 48, F= 13.723, p <0.001). Similarly, LSD analysis further revealed that field signs of Indian pangolin recorded on natural or wild habitat significantly differed from those which were on agricultural land and human vicinity area (p <0.001). The study concludes that the Indian Pangolin prefers habitats in the wild or natural area over those close to human vicinity and agricultural lands.