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Patterns of genetic variation along both latitudinal and elevational gradients have been intensively studied in the last few decades. To date, however, elevational patterns of genetic diversity and gene flow remain rarely compared for the same species along mountains at the center and edges of its latitudinal range. We used nuclear microsatellite analysis to compare the elevational patterns of both genetic variation and gene flow for Euptelea pleiospermum along elevational transects on the Qinling (33 degrees N; leading edge), Shennongjia (31 degrees N; mid-latitude), and Emei (29 degrees N; rear edge) Mountains in China. First, we found no elevational pattern of genetic diversity along the two marginal mountains, but we found higher genetic diversity in the middle-altitude populations than in the low- and high-altitudes along the mid-latitude mountain. Second, there was no obvious genetic structure along the two marginal mountains, but individuals along the mid-latitude mountain were clustered into the upper and lower groups. Third, the contemporary gene flow along the two marginal mountains was higher than that along the mid-latitude mountain. Lastly, we found no isolation-by-distance along all three mountains and a significant isolation-by-elevation along the mid-latitude mountain but not along the two marginal mountains. Our results demonstrated that the elevational patterns of both genetic variation and gene flow for a tree species are different along mountains at the core and edges of its latitudinal range. These differences are likely associated with the discrepancies in spatial isolation, ecological stability, and vegetation types, but not historical events (e.g., post-glacial recolonization) at different latitudes.