The community structure and diversity of endophytic bacteria in reed (Phragmites australis) roots growing in the Beijing Cuihu Wetland, China was investigated using the 16S rRNA library technique. Primers 799f and 1492r were used to amplify the specific bacterial 16S rRNA fragments successfully and construct the clone library. In total, 166 individual sequences were verified by colony PCR and used to assess the diversity of endophytic bacteria in reed roots. Phylogenetic analysis revealed that 78.9% of the clones were affiliated with Proteobacteria and included all five classes. Other clones belonged to Firmicutes (9.0%), Cytophaga/Flexibacter/Bacteroids (6.6%), Fusobacteria (2.4%), and nearly 3.0% were unidentified bacteria. In Proteobacteria, the Alpha and Gamma subgroups were the most abundant, accounting for approximately 34.4% and 31.3% of all Proteobacteria, respectively, and the dominant genera included Pleomorphomonas, Azospirillum, and Aeromonas. In addition, nearly 13.6% of the Proteobacteria were very similar to some genera of sulfate-reducing bacteria (SRB) such as Dechloromonas, Desulfovibrio, and Sulfurospirillum. The bacteria in these genera are considered to play important roles in the metabolism of nitrogen, phosphorus, sulfur, and some organic compounds in wetland systems. Hence, this study demonstrates that within the diverse bacterial communities found in reed roots, endophytic strains might have a strong potential to enhance phytoremediation by reed wetlands.