Genetic diversity and differentiation are revealed particularly through spatio-temporal environmental heterogeneity. Acer ginnala, as a deciduous shrub/small tree, is a foundation species in many terrestrial ecosystems of Northern China. Owing to its increased use as an economic resource, this species has been in the vulnerability. Therefore, the elucidations of the genetic differentiation and influence of environmental factors on A. ginnala are very critical for its management and future utilization strategies. In this study, high genetic diversity and differentiation occurred in A. ginnala, which might be resulted from its pollination mechanism and species characteristics. Compared with the species level, relatively low genetic diversity was detected at the population level that might be the cause for its vulnerability. There was no significant relationship between genetic and geographical distances, while a significant correlation existed between genetic and environmental distances. Among nineteen climate variables, Annual Mean Temperature (bio1), Mean Diurnal Range (bio2), Isothermality (bio3), Temperature Seasonality (bio4), Precipitation of Wettest Month (bio13), Precipitation Seasonality (bio15), and Precipitation of Warmest Quarter (bio18) could explain the substantial levels of genetic variation (> 40%) in this species. The A. ginnala populations were isolated into multi-subpopulations by the heterogeneous climate conditions, which subsequently promoted the genetic divergence. Climatic heterogeneity played an important role in the pattern of genetic differentiation and population distribution of A. ginnala across a relatively wide range in Northern China. These would provide some clues for the conservation and management of this vulnerable species. Genetic diversity and variation are manifested through phenotypic, chromosomal, and proteomic variations, which are revealed particularly through spatio-temporal environmental heterogeneity 1-3. Geographical topology can play a key role in determining genetic divergence of species 4-6. Climate conditions, in particular the most recent climatic oscillations, can also impact the evolution of the local organisms 7. Under the changing conditions, if species unable to respond the environmental change, it will be at increased risk of extinction 8. Indeed, species survival ultimately depends on its genetic diversity and variation 9. Thus, investigating the genetic diversity and extent of genetic differentiation within/between populations, while estimating the impact of environmental factors and understanding the processes that maintain these variations not only are very useful toward gaining deeper insights into evolutionary history, but also are critical for the prudent formulation of conservation, management and utilization strategies 2,3,10-13. Acer ginnala (Aaceraceae) is a deciduous shrub/small tree that has monoecious and anemophilous pollination with an outcrossing breeding system 14-16. It is a foundation species in many terrestrial ecosystems, distributing i...