To probe the distribution of ammonia-oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) in different ecosystem lake sediments, the abundance and community of AOA and AOB in freshwater sediments were investigated in eight mesotrophic or eutrophic lakes.AOA and AOB were ubiquitous in all sediments and the abundance of archaeal amoA gene in sediments of eutrophic lakes significantly outnumbered that in sediments of mesotrophic lakes while the abundance of bacterial amoA gene was equal in all sediments form these lakes.Phylogenetic analysis showed that all archaeal amoA sequences fell within either Crenarchaeotal Group (CG) Lib or CGI.1a subgroup, and all AOB clustered with genus Nitrosomonas or Nitrosospira.The great abundance of AOA instead of AOB appeared significantly in A-type lake sediments with the high density of Corbicula fluminea and the low contents of organic substances.Based on T-RFLP of amoA gene, the macrozoobenthos and organic substances could affect the AOA community structure in sediments.These findings represent the first detailed relationship between AOA and macrozoobenthos in freshwater lake sediments by demonstrating that AOA are positively correlated with the density of Corbiculafluminea.The different ecosystem types among lakes are the major factor to cause the differentiation of the ammonia-oxidizing prokaryotes.