Abstract  [Aim]  To investigate the genetic diversity of Apis cerana cerana populations across different geographical locations in Shaanxi and its adjacent areas, and to provide a reference for the conservation and utilization of A. cerana cerana genetic resources in Shaanxi. [Methods]  Whole-genome resequencing was carried out on 49 A. cerana cerana populations collected from western Shaanxi. The raw data was analyzed using PCA principal component analysis, ADMIXTURE population genetic structure analysis, phylogenetic analysis, and genetic variation analysis in combination with previous studies and GenBank public data. [Results]  Population genetic structure and PCA principal component analysis showed distinct genetic differentiation between the northern plateau population of Shaanxi and the central plain, western plain, western mountainous, and southern mountainous populations of Shaanxi. Genetic differences were also observed between WShxiPn and WShxiMt. Genetic variation analysis showed that the average F_st value between the NShxiPl and other populations in Shaanxi was 0.050 9. This value was higher than the average F_st value of 0.029 61 between populations in other geographical locations within Shaanxi. WShxiMt had a low F_st value of 0.039 7. In the adjacent areas, TailvMt also had a low F_st value of 0.044 3 similarly, a low F_st value of 0.022 1 was observed for WshxiPn and ShenFr. Compared with other populations, WShxiPn and WShxiMt had relatively high nucleic acid polymorphisms of 0.001 430 62 and 0.001 483 04, respectively. This indicates a relatively high level of genetic diversity within their populations. Phylogenetic tree analysis showed that WShxiMt, NShxiPl, and TailvMt shared a close genetic relationship, whereas WShxiPn was found to be closely related to ShenFr. [Conclusion]  A high level of genetic diversity was exhibited among the different geographical regions of Chinese bees in Shaanxi. There was pronounced genetic differentiation between populations in the northern plateau of Shaanxi and populations in other geographical regions of Shaanxi. Our analysis revealed two possible independent historical transmission routes for A. cerana cerana in Shaanxi. One route appeared to be in north Shaanxi, and the second in south Shaanxi. This study is the first of its kind to demonstrate the genetic diversity of A. cerana from the perspective of whole-genome resequencing. Additionally, we revealed the genetic relationship between different geographical locations. This study contributes valuable genetic information for the protection and utilization of germplasm resources of A. cerana in Shaanxi.