To investigate the effects of aquatic plants on ammonia-oxidizing bacteria (AOB) at their root zones, four species of aquatic plants were selected, Phragmites communis, Typha angustifolia L., Potamogeton crispus L., and Limnanthemun nymphoides, which were widely used in ecological restorations. AOB in the samples were enumerated by most-probable-number (MPN) method. Nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) procedures were performed with ammonia oxidizer-selective primers. Main DGGE bands were excised from the gel and sequenced for phylogenetic affiliation. Results indicate that AOB densities are always higher at the root zones of emergent plants (Phragmites communis 2.8 x 10(5) cells/g and Typha angustifolia L.4.3 x 10(5) cells/g) than those of submerged and floating-leaved plant (Potamogeton crispus L. 9.3 x 10(4) cells/g and Limnanthemun nymphoides 7.7 x 10(4) cells/g). At the root zones, the oxidation-reduction potential is above zero and NH4+ concentration is lower than it in the bare surface sediment. Fourteen major bands were recovered from the DGGE gel, re-amplified and sequenced. Although the identified bands have their respective similar sequences in GenBank, most of them are related to Nitrosomonas-like. This type of bacteria would play an important role of nitrogen cycle in lake sediment after ecological restoration.