Abstract: As an important component of the ecosystem, archaea play a crucial role in driving earth’s biogeochemical cycles. The estuary is a unique geographical transition zone located at the confluence of rivers and oceans. The esturay is considered as a natural testing ground for the study of the structure and diversity of archaeal communities, owing to its complex and changing hydrological environment. Here, we first introduced the development history and technical methods for archaeal research, including lipid structure analysis, fluorescence in situ hybridization, fluorescence quantitative PCR, and high-throughput sequencing. Then, we summarized the research progress on archaea in the estuary, as well as the main factors driving their distribution and community structure in estuaries, such as latitude, salinity and water depth. In addition, the ecological functions of several important archaea groups including ammonia oxidizing archaea, Bathyarchaeota and methanogenic archaea in the estuary were introduced. Finally, we proposed several future research directions of archaea in the estuary. A comprehensive understanding of the functions of the archaeal community in the estuary would be beneficial to the protection and the sustainable development of the estuary ecosystems.

Key words: archaea, estuary, community structure, distribution, ecological function.