Prokaryotes-driven ammonia oxidation plays an important role in global nitrogen cycling. The vertical distribution and diversity of ammonia oxidizing prokaryotes in a sediment core collected in Zhushan Bay, which is located in the northern part of Lake Taihu and being strongly influenced by heavy eutrophication and algae blooms. The samples were investigated by molecular approaches targeting at either the ammonia monooxygenase subunit A (amoA) or 16S rRNA gene. Our findings showed that both ammonia-oxidizing bacteria (AOB) and archaea (AOA) coexisted in the sediment profile. It was clearly indicated by denaturing gradient gel electrophoresis (DGGE) pattern that the dominating species of AOB shifted below 5 cm depth of the sediment core, highlighting the influences of key environmental factors, i.e. oxidation-reduction potential and NH+4-N, on AOB community; the dominance of Nitrosomonas oligotropha lineage sequences also suggested the environmental selection of AOB population in Lake Taihu. In contrast, the community composition of AOA in top 7 cm sediment was less variable. All retrieved archaeal amoA sequences belonged to either Soil & other environments or Marine & other environments lineages, which correspond to the CG1.1b and CG1.1a of Crenarchaeota, respectively. On the other hand, the anaerobic ammonium oxidizing (anammox) bacteria-like 16S rRNA gene sequences were retrieved at 5 cm depth only, which are distantly related to the known anammox bacteria. In this communication, we report for the first time a detailed simultaneous study on the three groups of ammonia-oxidizing prokaryotes in Lake Taihu sediment, which would enrich our understanding for ammonia oxidation process and nitrogen cycles in eutrophic lake ecosystems.