Objective Based on the REF6 and BRR2a genes, this study aimed to explore the distribution of the genetic diversity, the route of migration and the relationship between population genetic variation and environmental change of different populations of Populus davidiana.

Method After obtaining the CDS sequences of REF6 and BRR2a genes, we calculated the molecular diversity index, constructed the haplotype network maps and the phylogenetic trees of the different CDS sequences.

Result In the southwestern population, the mean of the three neutral tests for the REF6 and the BRR2a gene were negative, and the nucleotide polymorphisms were lower than those in both the northern and central populations. The result of phylogenetic tree and haplotype network maps showed that the outgroup first clustered with the northern population of P. davidiana. The southwest population tended to gather at the end, and the haplotypes of the two genes were abundant in the north and the central population. The haplotypes in the southwestern population were relatively single.

Conclusion P. davidiana migrates from the north to the south. In order to adapt to the climate of Yunnan-Guizhou Plateau, population located in the southwest region experiences strong natural selection, and local adaptation occurs in the southwest populations.