To understand better the mechanisms underlying the disjunct distribution of plants between Taiwan and Himalaya‐southwestern China, the genus Prinsepia (Rosaceae) was examined using phylogenetic and dating approaches based on molecular evidence. Prinsepia comprises four allopatric species with distributions in four subregions of China, i.e., P. scandens (southeastern China: Taiwan), P. sinensis (northeastern China: Heilongjiang, Jilin, Liaoning and E Inner Mongolia), P. uniflora (mainly northwestern China: Gansu, Henan, W Inner Mongolia, Ningxia, Qinghai, Shaanxi, Shanxi and Sichuan), and P. utilis (southwestern China: Guizhou, Sichuan, Xizang, Yunnan). Our phylogeny and molecular dating suggest that Prinsepia diverged into northern and southern clades in the Oligocene (ca. 32.61 mya); subsequently, the northern species pair split around 16.25 mya, and P. scandens diverged from the Xizang population of P. utilis in 11.89 mya but migrated to Taiwan later. We integrated different lines of evidence including phylogeny, molecular dating, geological history, and niche modelling, and conclude that divergence between the northwestern and northeastern species was caused by environmental differentiation (i.e., humidity/aridity), and the modern disjunctive distribution of the southern species pair was better explained by founder speciation/migration. We thus provide new insights into the origin of the disjunction between Taiwan and Himalaya‐southwestern China.