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Visual attractiveness and rarity often results in large carnivores being adopted as flagship species for stimulating conservation awareness. Their hunting behaviour and prey selection can affect the population dynamics of their prey, which in turn affects the population dynamics of these large carnivores. Therefore, our understanding of their trophic ecology and foraging strategies is important for predicting their population dynamics and consequently for developing effective conservation programs. Here we concentrate on an endangered species of carnivores, the snow leopard, in the Himalayas. Most previous studies on snow leopard diet lack information on prey availability and/or did not genetically check, whether the identification of snow leopard scats is correct, as their scats are similar to those of other carnivores. We studied the prey of snow leopard in three Himalayan regions in Nepal (Sagarmatha National Park (SNP), Lower Mustang (LM) and Upper Manang (UM) in the Annapurna Conservation Area, during winter and summer in 2014–2016. We collected 268 scats along 139.3 km linear transects, of which 122 were genetically confirmed to belong to snow leopard. Their diet was identified by comparing hairs in scats with our reference collection of the hairs of potential prey. We determined prey availability using 32–48 camera-traps and 4,567 trap nights. In the SNP, the most frequent prey in snow leopard faeces was the Himalayan tahr in both winter and summer. In LM and UM, its main prey was blue sheep in winter, but yak and goat in summer. In terms of relative biomass consumed, yak was the main prey everywhere in both seasons. Snow leopard preferred large prey and avoided small prey in summer but not in winter, with regional differences. It preferred domestic to wild prey only in winter, and in SNP. Unlike most other studies carried out in the same area, our study uses genetic methods for identifying the source of the scat. Studies solely based on visual identification of samples may be strongly biased. Diet studies based on frequency of occurrence of prey tend to overestimate the importance of small prey, which may be consumed more often, but contribute less energy than large prey. However, even assessments based on prey biomass are unlikely to be accurate as we do not know whether the actual size of the prey consumed corresponds to the average size used to calculate the biomass eaten. For example, large adults may be too difficult to catch and therefore mostly young animals are consumed, whose weight is much lower. We show that snow leopard consumes a diverse range of prey, which varies both regionally and seasonally. We conclude that in order to conserve snow leopards it is also necessary to conserve its main wild species of prey, which will reduce the incidence of losses of livestock. [ABSTRACT FROM AUTHOR]