Environmental heterogeneity in the Western Ghats (WG) is expected to drive both the assembly of endemic trees in extant assemblages and their long-term evolutionary dynamics. We addressed how (i) ecological strategies of endemic trees vary along current environmental gradients, (ii) environmental variations have shaped species’ distributions during the last glacial cycle, and (iii) their phylogenetic diversity varies across geographical and ecological space, under the influence of evolutionary processes.Methods: We assessed species’ traits related to reproduction, dispersal, and competitive ability, and characterized species potential distributions in present and past (Last Interglacial, LIG, Last Glacial Maximum, LGM) climatic conditions. We evaluated the extent of potential distribution changes through time, as a testimony of past pressures for migration, niche change or ecological plasticity. We quantified the phylogenetic diversity of endemic trees in mesoscale assemblages, which was expected to be lower in more stressful environments. We also tested the phylogenetic turnover of these assemblages with regard to geographic and environmental distances.Results: We identified three distinct scenarios of species’ responses to Quaternary climate changes– stability, contraction and shift. For high-elevation species, the cool, dry LGM was less restrictive than for medium-elevation and northern lowland species. Higher LIG seasonality restricted species requiring minimal seasonality. Phylogenetic diversity varied according to seasonality and historical climate stability, and was lower under longer dry seasons. The overall positive phylogenetic turnover was driven by annual rainfall and elevation gradients, but not space. High-elevation endemics were phylogenetically distinctive along the elevation gradient.Conclusions: The results concur to highlight the key role of environmental gradients in the biogeography and ecology of WG endemic trees. Palaeoclimate modelling reveals the likely local persistence of most endemics over the last 120 kyr, and their large spectrum of bioclimatic preferences reflect pre-Quaternary evolutionary events. Analyses of phylogenetic diversity further points to lower diversity in stressful conditions, which may reflect functional convergence. An abrupt change in phylogenetic turnover along the elevation gradient underlines the distinct biogeographic and evolutionary backgrounds of low- and high-elevation species pools.