Aim Investigating phytogeographical divides can help provide a better understanding of the evolution of floras. Tertiary relict floras in East Asia have been subdivided into a northern region (NEA) and a southern region (SEA), separated by an arid belt, although this division remains little-studied since it was proposed in 2002. To test its validity, we investigated the evolutionary history of a Tertiary relict species, Lindera obtusiloba. Location East Asia. Methods Chloroplast DNA (cpDNA) and nuclear microsatellites (nSSRs) were genotyped in 34 populations. Regional genetic diversities were compared, and genetic differentiation was calculated between and within regions. Bayesian phylogenetics and Bayesian clustering were employed for phylogeographic reconstruction. The time to the most recent common ancestor (TMRCA) and divergence time between the two regions were estimated. Historical rates of gene flow were calculated using the maximum-likelihood method. The potential habitat at present, during the Last Glacial Maximum (LGM) and during the Last Interglacial (LIG) were predicted by ecological niche modelling (ENM). Results Both markers revealed sharp genetic discontinuities and limited migration between regions. The TMRCA and population divergence can probably both be dated to the Pliocene. Clear genetic structure was found within each region. The genetic diversity of both markers and the age of chlorotypes decreased with increasing longitude within SEA. Japan harboured the highest genetic diversity within NEA, with abundant private and ancestral chlorotypes. NEA had greater genetic diversity than SEA in nSSRs, whereas the opposite was true for cpDNA. ENM in LGM and LIG may support long-term isolation in multiple locations in both regions. Main conclusions Our study provides solid evidence for the proposed floral subdivision along the arid belt within East Asia. Populations in both regions remained stable over a long period and sustained multiple glacial refugia. Westernmost SEA and easternmost NEA sustained ancestral populations. Clear eastward expansion was detected within SEA.