Abstract: Ammonia oxidation is the rate-limiting step in nitrification. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in ammonia oxidation. Sediments are important place for nitrogen circulation in lake. This study investigated the community diversity and abundance of AOA and AOB in the surface sediments of Donghu Lake and their relationships with environmental factors utilizing high-throughput sequencing and real-time quantitative PCR of ammonia monooxygenase (amoA) gene. The results showed that AOA and AOB were dominated by Nitrosopumilus and Nitrosomonas, respectively. There were significant correlations between the community structure of AOA and total nitrogen (TN) in sediments. AOB were significantly related to the contents of total organic carbon (TOC) and total phosphorus (TP). Additionally, AOA abundance was higher than that of AOB in the sediments. A significantly negative correlation between AOA abundance and temperature was detected, but there was no obvious change of AOB among the different seasons. These results implied that AOA could be the dominant driver in the ammonia oxidation in Donghu Lake.