The apparent absence of Himalayan low-elevation taxa in the central Indian region and resumption of their distribution in the high elevation of Western Ghats has puzzled biogeographers for several decades. Many theories have been proposed to explain this but attempts remain futile owing to insufficient empirical support. Here, we have employed a montane tree species, Rhododendron arboreum to investigate this pattern by integrating past ecological niche modelling with molecular signatures. Reconstruction of paleo-ecological niche from interglacial to Last Glacial Maxima (LGM) portrayed a gradual depletion of vegetation cover with extreme impoverishment in the Holocene. A similar pattern was also reflected from genetic signatures; population history revealed a very recent split between the Himalayas and Western Ghats in the late Quaternary. A few other tree species exhibiting the same disjunction demonstrated a similar modification of paleo-ecological niche from last interglacial. The study clearly indicated that the populations in the Western Ghats to be a relictual remnants of a once continuous distribution of R. arboreum.