Mountains are rich in endemic species diversity due to various factors, including steep elevational and climatic gradients and high habitat heterogeneity. While the causal factors behind high species endemism have been well worked out with respect to habitat characteristics and climate, the evolutionary mechanisms have received little attention. In this study, we attempt to decipher the evolutionary patterns of diversification of endemic plants in Nepal (Central Himalaya) and Bhutan (Eastern Himalaya) using species-presence records, phylogenetic supertrees, and ancestral area reconstruction methods. We found that the Nepal Himalaya was richer than Bhutan Himalaya with respect to endemic plant species. Maximum diversification of endemic plants in Nepal Himalaya occurred 35-20 million years ago (Mya), and in Bhutan Himalaya, it occurred during 55-45 Mya. Ancestral area reconstructions revealed that the maximum number of endemics in both Nepal and Bhutan Himalaya have diversified from taxa that migrated from Southeast Asiatic Malaysian and Southeast Chinese regions. We conclude that the plant species endemism in the Himalaya is closely linked with the phase-wise gradual uplift of mountains, long-term climate variation, species migration and floristic composition of the neighboring landscapes.