Simple SummaryResolving the taxonomic ambiguity of a species is important for their long-term conservation. We used non-invasive DNA sampling and camera trapping to address the taxonomic ambiguity in musk deer species in the Western Himalayas, and species occurrence locations were used to model the species distribution to identify suitable habitats. The combined results confirm the presence of only Kashmir musk deer (KMD) in the Western Himalayas. During our survey, no other musk deer species were found in the study area. This finding suggests that the presence of other species, such as Himalayan musk deer and Alpine musk deer, were incorrectly reported in the past. The predicted distribution (6% of the total area) of Kashmir musk deer is a narrow belt of the Western Himalayas between 2500 and 4500 m. Based on this study, we recommend long-term monitoring and assessment of KMD throughout its distribution range for its conservation and management.AbstractInsufficient research has been conducted on musk deer species across their distribution range, primarily because of their elusive behaviour and the fact they occupy remote high-altitude habitats in the Himalayas above 2500 m. The available distribution records, primarily derived from ecological studies with limited photographic and indirect evidence, fail to provide comprehensive information on the species distribution. Consequently, uncertainties arise when attempting to determine the presence of specific taxonomic units of musk deer in the Western Himalayas. This lack of knowledge hampers species-oriented conservation efforts, as there need to be more species-specific initiatives focused on monitoring, protecting, and combatting the illegal poaching of musk deer for their valuable musk pods. We used transect surveys (220 trails), camera traps (255 cameras), non-invasive DNA sampling (40 samples), and geospatial modelling (279 occurrence records) to resolve the taxonomic ambiguity, and identify the suitable habitat of musk deer (Moschusspp.) in Uttarkashi District of Uttarakhand and the Lahaul–Pangi landscape of Himachal Pradesh. All the captured images and DNA-based identification results confirmed the presence of only Kashmir musk deer (KDM) (Moschus cupreus) in Uttarakhand and Himachal Pradesh. The results suggest that KMD inhabit a narrow range of suitable habitats (6.9%) of the entire Western Himalayas. Since all evidence indicates that only KMD are present in the Western Himalayas, we suggest that the presence of other species of musk deer (Alpine musk deer and Himalayan musk deer) was wrongly reported. Therefore, future conservation plans and management strategies must focus only on KMD in the Western Himalayas.