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Palaeoclimatic conditions and the Palghat Gap (PG), an ancient geological break, influence structuring of genetic diversity in the Western Ghats (WG) of India. The present study describes the first approach of its kind on a plant species in the WG to decipher its evolutionary history by testing three hypotheses: (1) PG acts as a geographical barrier and forms two distinct phylogroups; (2) speciation and diversification occurred before Pleistocene glaciations; and (3) no distributional shifts have occurred since the late Pleistocene. The trnH-psbA and trnL-trnF markers were sequenced from leaf samples of Kingiodendron pinnatum collected from 14 populations across its geographical distribution. Two divergent haplogroups were found to the North and South of PG, with 13 and 12 haplotypes, respectively. A dated phylogenetic tree of haplotypes reveals the time of divergence between these groups as similar to 14.62 Mya. Diffusion analysis predicts the most probable origin of diversification to be in central Kerala. Niche modelling suggests that the potential distributional range of K. pinnatum in the present conditions covers a larger area than that predicted for the Last Glacial Maximum. Thus, only the first and second hypotheses are accepted. The predicted future distribution suggests that two subgroups in the southern group should be treated as evolutionarily significant units.