Plant speciation in mountain systems is crucial for shaping plant biodiversity, particularly for those endemic species with small populations. The mountain-geobiodiversity hypothesis (MGH) is among the possible mechanisms underlying mountain biodiversity. To test the MGH, we selected three Rhododendron species occupying the Hengduan Mountains (HDM) as focal species and then genotyped 12 populations using Restriction-site Associated DNA sequencing (RAD-seq) to reveal their speciation and divergence history. We found that there was high interspecific differentiation, low gene flow, and a high genetic drift among three Rhododendron species, suggesting that founder effects might play a key role in their differentiation. Historical gene flow occurred from R. brachypodum to R. calophytum var. pauciflorum. The effective population size of three Rhododendron species declined about 1 Kya ago. Rhododendron brachypodum experienced a bottleneck event during the Last Glacial Maximum (15–20 Kya). Three Rhododendron species diverged between 15.5 Mya and 3.13 Mya, which might be associated with the uplift of the HDM. These findings suggest that the speciation of three Rhododendron may be partly attributable to geological processes and climate fluctuations, strongly supporting the MGH. Additionally, our results provide new insights into the speciation patterns of endemic species and the protection of narrow-ranged species in mountain systems. © 2022 The Authors
