The Arctic and the Qinghai-Tibet Plateau (QTP) are two northern regions with the most extensive cold habitats on Earth and have undergone dramatic warming in recent decades. However, we know little about the historical connection of the Arctic and QTP biotas and their respective diversification processes. Here, we used Meconopsis and Oreomecon, an Arctic–QTP disjunct angiosperm genus pair with poor seed dispersal abilities, to shed light on the evolutionary connection of the Arctic and QTP floras and their respective diversification patterns. Our results show that the Meconopsis-Oreomecon clade colonized the Arctic from the QTP in the Late Eocene, suggesting the hitherto earliest known dispersal event between the two regions. The Arctic Oreomecon split from the QTP Meconopsis at ~34 Ma, associated with their climatic niche differentiation and aridification of the Asian interior. Although both Oreomecon and Meconopsis pre-adapted to open and low-temperature environments and had similar diversification patterns, they diversified asynchronously in respondence to different Cenozoic climate cooling events. The Arctic is approaching its carrying capacity, whereas the QTP is still far from saturation. These findings improve knowledge of evolutionary connection and difference between Arctic and QTP floras, and have important conservation implications given enhanced warming in both regions.