Aim: This study tests predictions of the central-marginal (C-M) hypothesis using geographical patterns of genetic variation in a Cenozoic relict tree species Euptelea pleiospermum. Additionally, we explore the extent to which post-glacial recolonization and landscape barriers created by topographical heterogeneity shape spatial genetic variation. Location: South-west and central subtropical China. Methods: Using microsatellite data of 678 individuals from 21 populations, we documented geographical patterns of genetic diversity and population genetic structure, supplemented with current and past (Last Glacial Maximum, LGM) distributions based on species distribution models (SDMs). Genetic structure was determined by non-spatial and spatially sensitive Bayesian clustering, analysis of molecular variance, barrier analysis and a multivariate population graphing approach. We also examined both historical and contemporary gene flow. Results: Genetic diversity significantly declined with distance from centre and showed unimodal patterns along both latitude and longitude. The C-M pattern of genetic diversity along latitudinal gradient is high-latitude-skewed, with the peak at higher portion of the species' latitudinal extent. The Sichuan Basin divided individuals into south and north clusters, whereas the Qinba Mountains did not. The general shape of the predicted distribution during the LGM is strongly similar with that of current distribution, except the Sichuan Basin. Main conclusions: Our study provides genetic evidence for the C-M hypothesis in a Cenozoic relict tree species across its distribution in China. The Sichuan Basin, rather than the Qinba Mountains, acts as dispersal barrier for a mountain tree species. Our results suggest that in situ refugia were maintained across southwest and central China during the LGM. The slight post-glacial northward expansion and asymmetrical south—north historical-gene flow did not result in a low-latitude-skewed C-M pattern of genetic diversity. Instead, complex topography in combination with the C-M dispersal dynamics shaped the latitudinal pattern of genetic diversity.