A study was conducted to determine the musk deer (Moschus chrysogaster) population, habitat structure, extent of poaching activities and the deer's current status in Manang district of Annapurna Conservation Area, Nepal. Results indicated that musk deer is distributed in all Village Development Committees (VDCs) of Manang districts except Phu VDC. The potential musk deer habitat in the study area covered 7.82 km² for Pisang VDC and 5.1 km² in Humde. It was estimated the populations were 23 animals in Humde and 27 in Pisang forest. The musk deer population trend has been declining at a high rate in all VDCs of Manang district, except Manang and Tanki Manang VDC. They preferred to occupy the 3300 to 3700 m altitudinal range in the study area, having 36 to 45 degrees angle of slope, a northwest and northern aspect, with good cover structure (dense forest). A high percentage of musk deer pellets were counted in forest land, followed by shrubland, grazing land and open land. A high percentage of pellets were counted in areas of 50 to 75% crown cover and 50 to 75% ground cover. In Humde, Betula utiliswas the most prominent tree species in the habitat while in Pisang VDC, Abies sp. was the most prominent. Snaring/trapping is currently the preferred method of poaching. Other threats to musk deer habitat include overgrazing by domestic livestock, forest fires, timber and other forest product collection.