Abstract: The abundance of amoA genes of ammonia oxidizing microorganisms in sediments from four lakes in central China was quantified using the quantitative polymerase chain reaction (qPCR), and their relationships with environmental factors were analyzed. The results showed that the number of amoA gene of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) was the most abundant in the Lake Xiaonanhu, with average values of 2.1×10^4and 2.8×10^3copies/g in the dry sediment, respectively. In the Lake Liangzi, only AOA were detected. The average gene number was 4.9×10^3copies/g for dry sediment. The mean number of AOA amoA gene in the lakes of Donghu and Tangxun was about 3.0×10^3copies/g. The average number of AOB amoA gene, however, was only 37and 86copies/g for the two lakes respectively. At all sampling sites, the number of amoA gene of AOA was about 3-278times that of AOB. The statistical analysis showed that both gene abundances of AOA and AOB increased with the increasing ρ(NH₄⁺) (for AOA, R=0.646, P<0.01; AOB, R=0.903, P<0.01), but AOB were more favored by this increase, resulting in a significant negative relationship between the ratio of AOA/AOB and ρ(NH₄⁺) (R=-0.685, P<0.01). Compared to the more positive effects of increased ρ(NH₄⁺) on AOB over AOA, a reverse negative impact of increased pH on ammonia oxidizing microorganisms was found. The abundance of amoA gene in the sediments was significantly and positively correlated with ρ(NO₃^-) in the pore water (for AOA, R=0.614, P<0.05; AOB, R=0.804, P<0.01). However, no significant relationship was found for ρ(NO₂^-) (P>0.05). Since a significant and negative relationship was found between ρ(NH₄⁺) and ρ(DO) (R=-0.641, P<0.008), the negative relationship between the abundance of amoA genes and ρ(DO) (for AOA, R=-0.520, P<0.05; AOB, R=-0.647, P<0.05) might be an indirect reflection of the intense association of ρ(NH₄⁺) and the abundance of amoA genes.