In this study, we performed 16S rRNA high-throughput sequencing to examine the diversity of endophytic bacterial communities in Gymnadenia conopsea growing at four different locations on Mount Sejila. The results revealed that a total of 715 920 effective sequences were obtained from all samples, which were associated with 2 365 operational taxonomic units, classified within five phyla, 38 families, and 62 genera. Proteobacteria was identified as the dominant bacterial phylum and the predominant genera were Pseudomonas, Methylbacterium, and Sphingomonas. Diversity analysis revealed that among the collected samples, the stem samples（LHS）collected at the Linhai Observation Deck were characterized by the highest endophytic bacterial community richness, whereas the richness of fruit samples（LDF）collected from the Radar Station was the lowest. The stem samples（FMS）from the Abandoned Wood Factory site were found to have the highest diversity of endophytic bacterial communities, and the diversity indices of communities in the stems, leaves, and fruits of plants growing at this sampling point（FM）at a lower altitude were higher than those recorded at the other three sampling points. Among the four types of tissue collected, the richness of endophytic bacterial communities in the stems, leaves, and roots was higher than that in the fruits, and we found that the diversity and richness of endophytic bacterial communities in fruits declined with increasing altitude, with the values obtained for the endophytic bacteria in fruit pods（LDF）being the lowest. Furthermore, we detected significant differences in the diversity of endophytic bacterial communities in the same tissue in different habitats, whereas there were differences in the diversity of endophytic bacteria within the different tissues of plants growing in the same habitat. Principal coordinate analysis indicated that the composition of endophytic bacterial communities was influenced by environmental factors and tissue types, and redundancy analysis and correlation heatmaps provided evidence to indicate that total phosphorus, total potassium, pH, and altitude were the main influencing factors, significantly correlated with the composition of these endophytic bacterial communities. Moreover, PICRSt prediction analysis revealed that the endophytic bacteria in G. conopsea were mainly enriched in three primary metabolic pathways, namely, metabolism, environmental information processing, and genetic information processing, and the activity of most of the identified metabolic pathways was found to show a declining trend with increasing altitude. This study employed high-throughput sequencing technology to analyze the effects of environmental factors and tissue types on the diversity and community structure of endophytic bacteria in G. conopsea. It aims to enrich and improve the resources of endophytic bacteria in wild G. conopsea, laying a foundation for the future resource development of beneficial endophytic bacteria and the protection of wild G. conopsea.