Studies on the impacts of macrophytes on the community structure and biodiversity index of ciliate protozoans were conducted in a shallow lake, Lake Biandantang during April 1996 to March 1997. Three kinds of habitats were selected, i.e., Habitat A (emergent + submerged macrophytes), Habitat B (only submerged macrophytes), and Habitat C (no macrophytes). A total of 88 species (belonging to 45 genera) of ciliates were identified. It was found that both the species number and the Margalef diversity index of ciliates were much higher in the macrophytic Habitats A and B (dominated by bactivorous and mixtrophic species) than in the non-macrophytic habitat C (dominated by bactivorous and algivorous); and that the richer species in the macrophytic habitats were mainly from the presence of many sessile species. The present study indicates that aquatic macrophytes support a diverse ciliate community by increasing the complexity of the trophic niches for these ciliates.