Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evoutionary history of a species, providing the premise for studying the response of organisms to rapid cimate change. However, for most species how exacty the spatial heterogeneity promotes popuation divergence and how genomic variations contribute to adaptive evolution remain poorly understood.

We examine the contributions of geographica and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as wel as genetic basis of local adaptation using RAD-seq and plastome data.

We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome‐environment association analyses identified 16 putatively adaptive loci mainly related mainly to biotic and abiotic stress resistance.

Our genome wide data provide new insights into the important roe of environmenta heterogeneity in shaping genetic structure, and access the footprints of ocal adaptation in an ancient reictual species, informing future conservation efforts.