[Context] Climate change is considered an important factor affecting the distribution and genetic diversity of species. While many studies have described the influence of climate change on population structure at various scales, little is known about the genetic consequences of a changing climate on endemic species. [Objectives] To assess possible changes in the distribution and genetic structure of the endangered Nilgiri tahr (Nilgiritragus hylocrius), which is endemic to the Western Ghats in India, under climate change and human disturbances. [Methods] We integrated tahr occurrence and nuclear DNA data with environmental geo-datasets to project the response of tahr populations to future climate change with respect to its distribution, genetic diversity and population structure. We screened the environmental variables using MaxEnt to identify a manageable set of predictors to be used in an ensemble approach, based on ten species distribution modelling techniques, to quantify the current tahr distribution. We then projected the distribution and genetic structure under two climate change scenarios. [Results] We found that suitable habitat for tahr (9,605 km2) is determined predominantly by a combination of climatic, human disturbance and topographic factors that result in a highly fragmented habitat throughout its distribution range in the Western Ghats. Under the severe high emissions RCP8.5 scenario tahr populations may lose more than half of their available habitat (55.5%) by 2070. Application of spatial Bayesian clustering suggests that their current genetic structure comprise four genetic clusters, with three of them reflecting a clear geographic structure. However, under climate change, two of these clusters may be lost, and in the future a homogenization of the genetic background of the remaining populations may arise due to prevalence of one gene pool cluster in the remaining populations. [Conclusions] Our interdisciplinary approach that combines niche modelling and genetic data identified the climate refugia (i.e., the remaining stable habitats that overlap with the current suitable areas), where the tahr populations would be restricted to small, isolated and fragmented areas. Essential factors to avert local extinctions of vulnerable tahr populations are a reduction of human disturbances, dispersal of tahr between fragmented populations, and the availability of corridors. This research was supported by the Department of Biotechnology, Ministry of Science and Technology, Government of India, and by a German Research Foundation (DFG) fellowship awarded to RK (project number 273837911). Peer reviewed