In order to provide reference for the protect, development and utilization of Vaccinium bracteatum resources, a total of 70 germplasm resources from 5 geographical populations were genotyped by GBS (Genotyping-by-Sequencing) technique to develop SNP markers. Using the developed markers, we investigated the genetic diversity and population genetic structure of V. bracteatum. The result shows a total of 9752 highly consistent and effective SNP markers were obtained through sequencing data analysis. 5 geographical populations of V. bracteatum all have high levels of genetic diversity, with an average effective number of alleles (Ne) of 1.52, expected heterozygosity (He) of 0.21, and observed heterozygosity (Ho) of 0.23. Among the 5 populations, the Liyang population had the highest genetic diversity. Analysis of variance for molecular variation(AMOVA) revealed that 64.45% of the total genetic variation resided among individuals. The fixation index (Fst) showed a high degree of genetic differentiation among the 5 geographical populations, with the highest Fst values(0.406) observed between the Liyang and Shangyou populations. Based on the results of NJ Phylogenetic tree, V. bracteatum resources clustered into three branches, which did not show obvious correspondence between geographical location and genetic relationships. The STRUCTURE analysis clustered the V. bracteatum resources into three subgroups, the results of principal component analysis was consistent with it, and different geographical populations are distributed in each subgroup, indicating the existence of high gene exchange in V. bracteatum resources. This study provides reference for selection and breeding of V. bracteatum and germplasm conservation.