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Aim: The Massenerhebung effect (Mass elevation effect) refers to heat‐ or wind‐driven altitudinal distribution patterns of temperature‐dependent parameters among massifs with narrower range and lower elevation around peripheral and isolated mountains compared to core and continuous ones. Although common in ecology, this effect is rarely discussed in population genetics. Here, we use genetic markers to reveal population genetic patterns and also test the mountain‐ and sky‐barrier hypotheses relevant to the Massenerhebung distribution pattern of Acer morrisonense in Taiwan's rugged topography and varied local climates. Location: The alpine and cloud forest of Taiwan. Taxon: Acer morrisonense Hayata. Methods: Two chloroplast DNA (cpDNA) fragments and 17 expressed sequence tag‐simple sequence repeat (EST‐SSR) loci, respectively, from 200 to 286 individuals were used to elucidate the phylogeographic pattern of pollen and seed dispersal of A. morrisonense. These data were combined with ecological niche modeling (ENM) to infer distribution range shifts and refugia. We also correlated the genetic‐divergence indices with spatial factors to clarify latitudinal and altitudinal effects on genetic diversity. Results: The incongruent phylogeographic patterns of genetic distributions between nuclear and cpDNA markers indicate unhindered pollen flow but spatially constrained seed dispersal. Taken together with ENM, the genetic pattern further reflects historical colonization from central‐mountain refugia to edges since the Holocene. The Massenerhebung reduces the gene flow by the surrounding mountains and also causes lower genetic diversity compared to central alpine populations. Main conclusions: This study is the first to reveal the influence of Massenerhebung effect on cpDNA genetic structure of montane trees and reflect the spatial trends of seed dispersal. This population genetic pattern can also be attributed to the demography‐related range shifts with paleoclimate fluctuations under complex mountain topography, supporting the mountain‐barrier hypothesis. The results have important implications for conserving the genetic diversity of species with a wide altitudinal distribution range. [ABSTRACT FROM AUTHOR]