High oxygen levels and root exudates together provide a resource-enriched habitat for rhizosphere microbes that, in turn, foster plant growth and perform key ecological functions. Plant genotype is a main factor shaping rhizosphere bacterial communities; however, the influence of plant genotype on the rhizosphere bacterial community of aquatic macrophytes remains unknown. Here we collected samples of the rhizosphere and bulk sediments of two genotypes of the macrophyte Phragmites australis from the littoral areas of freshwater lakes in China. High-throughput sequencing of the 16S rRNA gene was used to characterize the rhizosphere bacterial community. We found that the rhizosphere recruited a distinct bacterial community relative to that of the bulk sediment. The rhizosphere microbial community was characterized by distinct community composition and core OTUs comprising a few dominant taxa involved in the regulation of plant fitness and nutrient cycling. These taxa included Arthrobacter, Pseudomonas, Trichococcus, and Ramlibacter. Network analysis showed distinct co-occurrence patterns and a genotype-specific preference for hub taxa within the rhizosphere bacterial communities of each genotype. Functional analysis revealed difference between the relative abundance of functional groups participating in C, N, and S cycling. Our results improve our understanding of the composition of the rhizosphere bacterial community of aquatic macrophytes and highlight the importance of a comprehensive consideration of plant genotype in plant bioremediation in aquatic ecosystems.