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The climatic shifts in the Quaternary Period acted as an important driving force for evolution of the world's biodiversity. In this study, responses to the ice age of a rare and endangered tree of Indian Western Ghats, Syzygium travancoricum, was investigated through a combination of molecular data and ecological niche modeling.Results indicate the moderate (nrDNA) to high (cpDNA) population structure, presence of private alleles, and absence of phylogeographic structure. Spatial distribution of diversity does not signifi- cantly support southern colonisation, nor the Palghat Gap as a geographical barrier based on the genetic structure. Combined insights from Ecological Niche Modelling and population history de- picts a probable colonisation of the Western Ghats in the late Miocene or later followed by a split into separate southern and northern populations from the middle to late Pleistocene. The prevalence of favourable conditions in the post-Last interglacial period stimulated rapid population expansion and a very recent decline. The absence of phylogeographic structure and overall climatic stability from Last Interglacial do not offer support to an existence of refugia in the Western Ghats. We con- clude by discussing appropriate conservation measures for this rare and endangered tree based on our findings.