Abstract Habitat fragmentation can facilitate local adaptation of species to heterogeneous environments and affect population demographic history. To understand the factors influencing evolutionary dynamics, such as climatic fluctuations and complex geomorphological features, we used 18 chloroplast microsatellites, 15 nuclear microsatellites, three chloroplast fragments, and two nuclear regions to explore the genetic structure and phylogeographical history of Pseudotaxus chienii. Furthermore, its current and past distributions were constructed based on ecological niche modelling. Moderate to high levels of genetic diversity were found at the species level. Precipitation was a decisive factor influencing the genetic structure of P. chienii. In addition, local adaptation to heterogeneous environments also contributed to maintain the fragmented distribution. Finally, incomplete lineage sorting led to the cyto-nuclear discordance. Overall, we show that pre-Quaternary and Quaternary climatic fluctuations and restricted gene flow exerted significant effects on the formation and maintenance of the fragmented distribution of P. chienii. The study provides new insights into the evolutionary history of plants in subtropical China.