Climate change strongly influences species distributions and population genetic structure, but independent analyses of these factors often yield uncertain conclusions. To address this, we developed an integrative framework combining population genetics and dynamic species distribution modelling (DSDM) to reconstruct the post-glacial history of black pepper (Piper nigrum) in the Western Ghats, India. Genetic analyses of 243 individuals from 14 wild populations using six chloroplast and five nuclear SSR markers revealed higher gene diversity, haplotype richness, and allelic richness at lower latitudes, and identified two major phylogeographic groups in the southern and central Western Ghats. Demographic inference from chloroplast SSRs suggested these groups diverged around the Last Glacial Maximum (LGM, 21,000 years BP). DSDMs, applied at high spatial (1 km) and temporal (100-year) resolution, initially showed high uncertainty in model parameters, which was substantially reduced when combined with genetic data in a genetically informed DSDM. This model maximized the correlation between genetic diversity and simulated colonisation history, revealing a northward expansion from low-latitude refugia and recent range fragmentation. The correlation between genetic diversity and colonisation time was stronger than with latitude, highlighting the value of integrating genetic data with DSDMs. Overall, this approach reduces uncertainty in species distribution predictions and improves the interpretation of population genetic patterns, offering insights not accessible when these methods are applied independently.