BackgroundLeymus secalinusis a pioneer plant grown in the Zoige desertified alpine grassland and it is also one of the dominant plant species used for environmental remediation.L. secalinusplays a large role in vegetation reconstruction in sandy land, but the abundance and diversity of its endophytes have not yet been investigated.ObjectivesThis study was performed to investigate the changes in the endophytic bacterial community structure ofL. secalinusunder different ecological environments and to analyze the effects of environmental changes and different plant tissues on theL. secalinusendophytic bacteria.MethodsLeaf, stem, and root tissue samples ofL. secalinuswere collected from Zoige Glassland (Alpine sandy land) and an open field nursery (Control). DNA was extracted and the 16S ribosomal DNA was amplified. The sequence library was sequenced on an Illumina MiSeq platform and clustered by operational taxonomic units (OTUs).α-diversity andβ-diversity analyses, species diversity analyses, functional prediction, and redundancy (RDA) analyses for the soil physicochemical properties were conducted.Resultsα-diversity andβ-diversity analyses showed that the endophytic bacteria inL. secalinusvaried in different areas and tissues. The abundance ofAllorhizobium-Neorhizobium-Pararhizobium-Rhizobium, which is related to nitrogen fixation, increased significantly in theL. secalinusfound in the Zoige Grassland.Moreover, the abundance of nutrition metabolism and anti-stress abilities increased in functional prediction in the desert samples. The soil physicochemical properties had an insignificant influence on bacterial diversity.ConclusionThe changes in the endophytic bacterial community structure inL. secalinuswere significant and were caused by environmental alterations and plant choice. The endophytic bacteria inL. secalinusgrown in alpine sandy land may have greater anti-stress properties and the ability to fix nitrogen, which has potential value in environmental remediation and agricultural production.