Abstract: The study conducted an integrated analysis combining traditional culture dependent isolation with Illumina high-throughput sequencing from 17 sampling sites across the Lhalu Wetland in Xizang to investigate the community structure of root endophytic bacteria in Phragmites australis. The potential ecological functions of these bacterial communities were predicted using the FAPROTAX database. This study aims to elucidate the resource characteristics of endophytic microorganisms associated with this key plant species in a high-altitude urban wetland. The findings indicated that the high-throughput sequencing annotated a total of 53 phyla, 131 classes, 290 orders, 451 families, and 1,032 genera. The dominant phyla were Proteobacteria, Actinobacteriota, and Firmicutes, while the dominant genera were Pseudomonas and Aeromonas. In contrast, the culture-dependent method yielded 424 isolates, which were classified into 2 phyla, 4 classes, 7 orders, 9 families, 18 genera, and 58 species. The predominant cultivated groups were the phylum Proteobacteria, the class Gammaproteobacteria, and the genus Pseudomonas. Functional prediction indicated that the endophytic bacterial community possesses 35 potential ecological functions, predominantly chemheterotrophy.