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Zootherapy is accepted all around the globe not only in ancient cultures but different animal derived medicines are also part of the practice in the modern health care systems. The present study assessed the traditional ethnozoological usage of wild animals by local inhabitants in Ladakh region, India, and the reference data for scientific approaches for protection of faunal diversity in trans-Himalayas. The ethnozoological documentation of the animals in Ladakh was carried out through semistructured and close-ended questionnaire surveys and interviews. Multivariate ecological community analysis was used to elucidate the relationship between ethnozoological usage and animal species. Our results showed three animal usage clusters with 32% similarity. Moreover, the similarity in animal usage between digging tools, trophy, handle of tools, decoration, and matting, showed less than 32% of similarity. The highest priority of local people was for food followed by decoration and medicinal usage. The most frequently used animal parts were meat followed by fur and horn. Medicinal uses of 48% of the reported species, i.e., Alectoris chukar (chukar), Cuon alpinus (Asiatic wild dog), Lepus oiostolus (hares), Marmota himalayana (marmots), Ovis aries vignei (Ladakh urial), Pantholops hodgsonii (Tibetan antelope), Procapra picticaudata (Tibetan gazelle), Pseudois nayaur (blue sheep), Tetraogallus himalayensis (Himalayan snow), Tetraogallus tibetanus (Tibetan snow cock), and Lutra lutra (common otter) were reported for the first time from this region. Our study provides innovative information regarding the ethnozoological knowledge in the Ladakh region and reference data for policymakers, researchers, land managers, common public, and the other stakeholders to develop logical and scientific approaches for sustainable use of faunal diversity in hotspot regions like trans-Himalayas and other similar biodiversity-rich sites.