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P>1. Community structures of planktonic ammonia-oxidising archaea (AOA) and bacteria (AOB) were investigated for five high-altitude Tibetan lakes, which could be classified as freshwater, oligosaline or mesosaline, to develop a general view of the AOA and AOB in lakes on the Tibetan Plateau.

2. Based on PCR screening of the ammonia monooxygenase alpha-subunit (amoA) gene, AOA were present in 14 out of 17 samples, whereas AOB were detected in only four samples. Phylogenetic analyses indicated that the AOB communities were dominated by a unique monophylogenetic lineage within Nitrosomonas, which may represent a novel cluster of AOB. AOA, on the other hand, were distinct among lakes with different salinities.

3. Multivariate statistical analyses indicated a heterogeneous distribution of the AOA communities among lakes largely caused by lake salinity, whereas the uniform chemical properties within lakes and their geographical isolation may favour relatively homogeneous AOA communities within lakes.

4. Our results suggest a wide occurrence of AOA in Tibetan lakes and provide the first evidence of salinity-related differentiation of AOA community composition as well as potential geographical isolation of AOA in inland aquatic environments.