Endophytic bacteria are widely distributed in various tissues and organs of plants and play various roles in the growth of plants. Moreover, the role of endophytic bacteria in plant seeds on plants has attracted more and more attention. In this paper, seeds of Hippophae rhamnoides subsp. sinensis in Yuzhong County and Qin'an County were used as materials to analyze its endogenous bacteria diversity, in order to explore the impact of habitat on the endogenous bacteria diversity of Hippophae rhamnoides subsp. sinensis seeds and to provide a basis for further research on the interaction between Hippophae rhamnoides subsp. sinensis and endophytic bacteria. The diversity of endophytic bacteria in Hippophae rhamnoides subsp. sinensis seeds was analyzed by plate culture method and high-throughput sequencing method. The endophytic bacteria isolated from plate culture method were identified by 16S rRNA gene sequence analysis combined with morphological characteristics. For high-throughput sequencing data based on the analysis of Operational Taxonomic units species annotation. Four strains of endophytic bacteria were isolated from the seeds of Hippophae rhamnoides subsp. sinensis in Yuzhong County by plate culture method, which were classified into Bacillus, Staphylococcus and Pseudomonas. Five strains of endophytic bacteria were isolated from the seeds of Hippophae rhamnoides subsp. sinensis in Qin'an County, which were classified into Bacillus, Staphylococcus and Acinetobacter. The endophytic bacteria of Hippophae rhamnoides subsp. sinensis seeds in Yuzhong County belong to 7 phyla and 68 genera and the endophytic bacteria of Hippophae rhamnoides subsp. Sinensis seeds in Qin'an County belonging to 5 phyla and 30 genera were detected by high throughput sequencing. Among them, at the phylological classification level, the main dominant phylum of endophytic bacteria from Hippophae rhamnoides subsp. Sinensis seeds in Yuzhong County were Cyanobacteria and Proteobacteria, with relative abundance of 95.62% and 2.03%, respectively. The main dominant phyla of Hippophae rhamnoides subsp. Sinensis seeds in Qin'an County were Proteobacteria and Cyanobacteria, with relative abundance of 91.68% and 8.06%, respectively. At the level of genus classification, the dominant endophytic of Hippophae rhamnoides subsp. sinensis seeds in Yuzhong County was Cyanobacteria with a relative abundance 95.09%. The dominant endophytic of Hippophae rhamnoides subsp. Sinensis seeds in Qin'an County was Stenotrophomonas with a relative abundance of 85.60%. The endophytic bacteria of Hippophae rhamnoides subsp. Sinensis seeds in Yuzhong County and Qin'an County were rich in diversity. The diversity and richness of endogenous bacteria were obviously different. The diversity and richness of endophytic bacteria in seeds of Hippophae rhamnoides subsp. Sinensis were higher in Yuzhong County than those in Qin'an County.