To understand the effects of invasive plant Flaveria bidentis on nitrification processes, the community structures of soil ammonia-oxidizing archaea (AOA) were investigated using the method of PCR-DGGE in a Flaveria bidentis invaded habitat in Jinghai County of Tianjin, China. The results showed that the diversity of AOA community tended to increase with F. bidentis invasion. The Shannon diversity indexes (H) of AOA were in an order of invaded bulk soil > invaded rhizosphere soil > non-invaded soil, with significant differences detected. Ammonium nitrogen and pH value were the key factors determining the community structure of AOA. All identified AOA belonged to Nitrososphaera cluster, the presence of specific ammonia-oxidizing archaea mainly contributed to higher diversity of AOA found in F. bidentis-invaded soil.