Recent evidence from natural environments suggests that in addition to ammonia-oxidizing bacteria, ammonia-oxidizing archaea (AOA) affiliated with Thaumarcheota, a new phylum of the domain Archaea, also oxidize ammonia to nitrite and thus participate in the global nitrogen cycle. Besides natural environments, modern data indicate the presence of amoA-encoding archaea (AEA) in wastewater treatment plants (WWTPs). To further elucidate whether AEA in WWTPs are AOA and to clarify the role of AEA in WWTPs, this paper reviews the current knowledge on this matter for wastewater engineers and people in related fields. The initial section coveys a microbiological point of view and is particularly based upon data from AOA cultures. The later section summarizes what is currently known about AEA in relation to WWTPs. Based on the reviewed data, future research pathways are proposed in an effort to further what is known about AEA in wastewater treatment systems.