Aims Malus sieversii, being listed as a national second-class protected plant in China, is recognized as one of the wild ancestors for domesticated apple. It is fragmentally distributed in arid mountains of the Central Asian. Here, we aimed to investigate the main environment variables shaping population genetic variations and the genetic adaptation in response to these environment variables for this species. MethodsWe collected ten M. sieversii populations from Yili Prefecture of China, Kazakhstan and Kyrgyzstan. Single nucleotide polymorphism (SNP) dataset was generated by SLAF-seq. Population genetic structure was inferred using the ADMIXTURE software and principal component analysis. Main environment variables shaping population genetic variations were assessed by gradient forest analysis and redundancy analysis. Tests of associated outlier loci with environmental variations were carried out by latent factor mixed models, which was used to access genetic signatures of local adaptation.Important findings Ten populations were clustered into two lineages. Lineage A dominated eastern populations, while Lineage B mainly distributed in western populations. Two lineages were mixed in central populations, and an obvious pattern of geographical substitute along the longitude direction was found. The most important environment variables that influence the change of allele frequency for M. sieversii populations were temperature annual range (bio 07) and temperature seasonality (bio 04). Fifteen loci having a significant association with environmental variables were successfully annotated. Most of them were genes related to abiotic stress responses and stress-induced physiological adaptations, such as drought, salt and cold. In conclusion, temperature variation is the main factor that drives the adaptation of M. sieversii to environments. Physiological adaptations, as