A field study was conducted in two adjacent shallow lakes (Aiwan Lake and Qingnian Lake) in Tianjin, China, to investigate the effects of plant species and growth strategy (single or mix) on the microbial community’s structure and diversity in the rhizosphere of emergent plants by phospholipid fatty acid (PLFA) methods. The results demonstrated that microbial biomass was higher in the Typha orientalis (T. orientalis) rhizosphere than that in the Phragmites australis (P. australis) rhizosphere, whether they grew separately or together. The bacterial population of gram-positive bacteria (G⁺) was found to be less than that of the gramnegative bacteria (G^-) in all samples, and the ratio of G⁺ to G^- in the plant rhizosphere was less than that in the non-rhizosphere. The diversity index of plant rhizosphere was higher than that of the non-rhizosphere, and was higher in the T. orientalis rhizosphere than in the P. australis rhizosphere. Cluster analysis demonstrated that microbial community structure was more significantly influenced by plant species than by growth strategy.