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Himalayan Musk deer, Moschus chrysogaster is widely distributed but one of the least studied species in Nepal. In this study, we compiled a total of 429 current presence points of direct observation of the species, pellets droppings, and hoofmarks based on field‐based surveys during 2018–2021 and periodic data held by the Department of National Park and Wildlife Conservation. We developed the species distribution model using an ensemble modeling approach. We used a combination of bioclimatic, anthropogenic, topographic, and vegetation‐related variables to predict the current suitable habitat for Himalayan Musk deer in Nepal. A total of 16 predictor variables were used for habitat suitability modeling after the multicollinearity test. The study shows that the 6973.76 km² (5%) area of Nepal is highly suitable and 8387.11 km² (6%) is moderately suitable for HMD. The distribution of HMD shows mainly by …