Aim: Understanding the relative roles of geography and ecology in driving speciation, population divergence and maintenance of species cohesion is of great interest to molecular ecology. Closely related species that are parapatrically distributed in mountainous areas provide an ideal model to evaluate these key issues, especially when genomic data are analyzed within a spatially and ecologically explicit context. Here we used three closely related species of Primula that occur in the Himalayas, the Hengduan Mountains and Northeast Qinghai-Tibet Plateau (QTP) to examine spatial and ecological effects on interspecific divergence and maintenance of species cohesion. Location: Himalayas, the Hengduan Mountains and Northeast QTP Methods: We used genomic data for 770 samples of the three species using double-digest restriction site-associated DNA (ddRAD) sequencing and combined approximate Bayesian computation (ABC) modeling, generalized linear mixed modeling (GLMM) and niche-based species distribution modeling (SDM). Results: The three species are clearly delimited by the RADseq data. Further ABC modeling indicates that P. tibetica diverged first followed by a later divergence between P. nutans and P. fasciculata. The time frames of the divergences among the three species coincide with the uplifts of the Hengduan Mountains and the northern QTP during the late Miocene and Pliocene followed by a long period of founder events. SDMs indicate that the three species might have survived in different refugia during glaciations and came into secondary contact during the postglacial expansions but with no significant introgression. Finally, GLMM suggests that both the geographical and ecological factors play roles in population differentiation in P. fasciculata and P. tibetica, while for P. nutans, geography is the major driver of genomic variation. The different roles played by geographical and ecological factors in the three species may have affected the maintenance of species cohesion. Main conclusion: Our results provide insights of unprecedented details into the start and maintenance of interspecific divergence in the context of changing environments in mountains. Our findings highlight the significance of combining population genomics with environmental data when evaluating the effects of geography and ecology on interspecific divergence and maintenance of closely related species.