Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contribute significantly to the nitrogen cycle. The community structure of AOA and AOB is diverse in the different wetlands. Few studies have comparatively investigated the community structure and dynamics of ammonia-oxidizing organisms in the marsh wetland (Sanjiang wetland) and inland saline-alkaline wetland (Zhalong wetland) in Northeast China. In this study, soil samples were collected from two wetlands with different soil properties in July and October. The community structure of AOA and AOB based on the amoA gene was investigated by high throughput sequencing. The result showed that AOA affiliated to the Nitrososphaera lineage (1.1b group) were the dominant AOA in both Sanjiang and Zhalong wetlands, while AOB belonging to the Nitrosospira lineage was the dominant AOB in the Sanjiang wetland. AOB belonging to the Nitrosospira lineage and Nitrosomonas lineage were the dominant AOB in the Zhalong wetland in July and October, respectively. The dominant AOA and AOB in the Sanjiang wetland had no obvious variation from July to October, but the AOA and AOB communities in the Zhalong wetland changed a lot from July to October. Shannon and Simpson indexes showed the diversity of AOA in the Zhalong wetland was higher than that in the Sanjiang wetland, but the diversity of AOB in the Zhalong wetland was lower than that in the Sanjiang wetland. Nitrate (NO) and ammonium (NH) concentration and pH were the most significant factors influencing the community structure of AOA and AOB.