Himalayan musk deer(Moschus chrysogaster), commonly known as Kasturi mriga is listed as an endangered species by IUCN and protected by the National Park and Wildlife Conservation Act 1973 of Nepal. The study was carried out in two village development committees within the Annapurna conservation area region- Ghandruk and Shikha. Plots were laid using random sampling, and the corresponding GPS coordinates were recorded. The habitat of musk deer was analyzed through land cover analysis and vegetation analysis. Ivelv’s electivity index (+1 to -1) was calculated to determine the preference or avoidance of habitat by musk deer, in which positive values showed preference and negative values showed avoidance. The vegetation analysis was performed by applying the importance value index. The habitat map based on preference and avoidance was prepared using GIS. M. chrysogastershowed higher preference to the slope ranging from 25º to 35º (IV- 0.29), followed by the slope 15º to 25º (IV- 0.16). North-west aspect and North aspect had the IV values of 0.51 and 0.42 respectively that showed the greater predilection of musk deer to these aspects. Musk deer was widely distributed in the altitudinal range of 3400m to 3600m (IV- 0.27) that was followed by the altitude of 3300m to 3400m (IV- 0.26). Musk deer preferred the shrub land and grassland in maximum extent. The study sites were dominated by Birch- Rhododendron forest, which were widely used by the musk deer. The preferred plants were Rosa spp., Betula spp., Abies spp. whereas the herb species mostly consisted of Lichen/Moss and Khar/grass. The habitat map showed a notably smaller extent of preferred area, indicating an obligation towards conservation of the species in its present habitat. Regular patrolling and investigation of musk deer habitat and effective conservation strategies regarding habitat management is recommended.