Aquatic plant species greatly differ in the capacities to excrete oxygen and execute organic compounds into the rhizosphere environment. Accordingly, the difference in plant species and community composition may affect microbial community differently. In order to test this hypothesis mentioned above, the current study established five plant species richness levels (0, 1, 2, 3 and 4 species/microcosm unit) in vertical flow microcosm wetlands using a completely random block design, and irrigated the microcosms with Hoagland inorganic nutrient solution. The results showed that the microcosms monocultured with Rumex japonicus or Oenanthe hookeri showed a greater capacity of microbial communities to utilize amines/amides or miscellaneous compounds than the microcosms monocultured with Phalaris arundinacea or Reineckia carnea. Plant species richness not only increased microbial biomass carbon and nitrogen as well as dehydrogenase activity in the microcosms, but also enhanced the capacities of microbial communities to utilize carbohydrates and amino acids. Furthermore, the presence or absence of O. hookeri, P. arundinacea or R. carnea within a given plant community affected the capacity of microbial communities to utilize carbohydrate, miscellaneous and amines/amides.