Abstract: To investigate the seasonal changes of AOB and AOA and its relation with environmental factors in Sinonovacula constricta pond, AOA and AOB abundance in water and sediments were studied by fluorescence quantitative PCR with the functional gene amoA as a molecular marker. The results showed that the abundance of AOA in each season was one order of magnitude higher than that of AOB, and seasonal variation had certain effects on the abundance of AOA and AOB amoA genes in the water environment and sediments. In the water environment, AOB was significantly higher in autumn than the other three seasons (P<0.05), AOA in winter was the lowest and it was significantly lower in spring and autumn (P<0.05). In the sediment, AOB and AOA were significantly higher in winter than those in the other three seasons (P<0.05). Correlation analysis of environmental factors showed that AOB content in water was positively correlated with \rmNH_4^ + (P<0.05), but negatively correlated with \rmNO_2^ - (P<0.05). The abundance of AOA in water was positively correlated with water temperature (P<0.05), but negatively correlated with \rmNO_3^ - (P<0.05). In the sediment, the abundance of AOB was positively correlated with DO, \rmNO_3^ - , TN and \rmNO_2^ - (P<0.05), and negatively correlated with water temperature (P<0.05). The abundance of AOA was positively correlated with DO, TN and \rmNO_3^ - (P<0.05), and negatively correlated with water temperature (P<0.05). The results of multiple linear regression equation showed that the abundance of AOA and AOB in Sinonovacula constricta pond was significantly affected by \rmNO_3^ - . The results showed that AOA dominated the ammonia-oxidation process in the pond of Sinonovacula constricta, and the abundance of AOA and AOB was affected by salinity, temperature, nitrogen concentration, dissolved oxygen and other environmental factors.