The abundance and diversity of amoA gene, a gene putatively encoding ammonia monooxygenase subunit A, was evaluated in oxic lake water and anoxic sediments from two adjacent sites of Qinghai Lake, China. An integrated approach was employed including geochemistry, clone library construction, and reverse-transcription quantitative polymerase chain reaction. Whereas ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) in oxic lake water, the opposite was true in anoxic sediments. The AOB community was the same in the water and sediments and consisted of Nitrosomonas- and Nitrosospira-like sequences, suggesting that the sediment-associated AOB may be derived from the water column, but metabolically inactive. In contrast, the AOA community was distinct between the water column and the sediments, and clone sequences were related to those from aquatic environments and soils, respectively, suggesting that AOA in the sediments may be native and metabolically active. Our data have important implications for a better understanding of the potential role of ammonia oxidizers in lake ecosystems.