The knowledge of distribution and habitat use of a species, whose conservation status are under concern, is crucial to get information useful to establish any conservation plan. The Scaly ant-eater (Manis crassicaudata) is an “Endangered” insectivore lacking vital ecological studies in the Asian region. The current study investigated its distribution, abundance and habitat use in the Margalla Hills National Park, Islamabad. The animal species showed a patchy distribution in the park ranging from 462m to 1046m above sea level. The depths of its two types of burrows (feeding and sleeping) and the numbers of active and inactive sleeping burrows were found significantly different (p< 0.05, and p < 0.01, respectively). A very low population density (0.36/km2) of the Scaly ant-eater was recorded in the park.  Vegetation analysis of the study area revealed Dalbergia sissoo, Acacia modesta, and Pinus roxburghii as dominant trees, Dodonaea viscosa and Lantana camara as dominant shrubs and Cynodon dactylon as dominant herb species. The Scaly ant-eater showed a phyto-association with Lantana camara, and Punica granatum for making its permanent burrows, and Dalbergia sissoo and Acacia modesta tree speciesfor obtaining its insect food.