To investigate the distribution characteristics of ammoniaoxidizing archaea (AOA) in sediments of shallow lakes, we chose the shallow lakes in the Lixia River area, which is in the lower Huaihe River Basin, as the research object and studied the community structure of AOA in four shallow lakes with different functional types in the region using the methods of molecular biology and microbiology. The results show that there exists AOA in this region and this provides an important supplement to the global geographic distribution and habitat of AOA. In the surface sediments of this region, the diversity and richness of AOA is highest in the center of Dazong Lake. AOA is mainly accumulated in the groups 1.1b and 1.1a, in which, 71.3％ of the sequences belong to Group 1.1b and 28.7％ of the sequences belong to Group 1.1a. The presence of submerged plants significantly improves the richness of Group 1.1b, and abundant organic matter is conducive to promoting the growth of AOA. The surrounding factories, sandpits, fisheries, and the livestock breeding upstream of Jiulongkou affect the characteristics of the community in the surface sediments.