Anthropogenic climate change has been identified as one of the main threats to current biodiversity, particularly for mountain species, which are especially sensitive to reductions of suitable habitat. Climate change impact assessments through correlative models have become a widely used tool for evaluating vulnerability of species to global warming. However, interpreting these results in an evolutionary context is essential to understand the phylogenetic structure of the predicted impact, as well as the potential evolutionary responses. The present study evaluates the impact of climate change on the Andean-Patagonian genus Onuris, interpreting the effect on its species and main phylogenetic groups. We first estimated a species phylogeny using both nuclear ribosomal and plastid data, which was then used to interpret the evolution of climatic niches and characterize the vulnerability of different species, evolutionary significant units (ESUs), and main lineages to climate change. Evaluations were conducted at the species level using species-specific metrics and at the genus level with emergent metrics such as richness, phylogenetic diversity, and shared response to local extirpation. Analyses showed that closely related species exhibit greater climatic niche similarity, suggesting a possible pattern of phylogenetic niche conservatism for divergence in the genus, with the greatest niche divergence recovered between lineages distributed in central-northern and southern Andean-Patagonian region. Species and ESUs of the lineage distributed in the southernmost portion of Patagonia (ca. 47°S–55°S) were most negatively affected under the different scenarios and models tested. The results also indicated a greater impact on richness than on phylogenetic diversity, mainly due to the establishment of the northern lineage in future projections over the range of the southern lineage. However, predictions show a pronounced negative effect of climate change for the entire genus. Likewise, results obtained suggest the high vulnerability of the current biota in the southern end of the Andean-Patagonian region.