Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite (CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction (PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2.42 x 10(6) copies x g(-1) dry sludge and 6.51 x 10(6) copies x g(-1) dry sludge, respectively. The abundance of AOA in biofilm was 10.1-14.1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1.8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5.2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8.1, subcluster 4.1, subcluster 1.1 and Nitrosopumilus subcluster 5.2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system.