Abstract: 【Objectives】 Soil acidification caused by over application of N fertilizers has posed a great challenge for apple security production. Nitrification is a central process of soil nitrogen cycle, which is driven by ammonia-oxidizing microorganisms, including ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Studying the correlation of the abundance of gene fragment amoA with the potential nitrification (PN), as well as the soil physical and chemical properties, will be of help to objective evaluation of soil ammonia-oxidizing microorganisms in soil ecological system.【Methods】 Two apple orchards in east of Liaoning Province were used for investigation, in both of the orchards, apple cultivar was ‘hanfu’. In one orchard, the weeds had been removed every year (D1) and in the other the weeds had been cut and returned to soil (D2). Soil samples were collected on April 28th (budding period), July 24th (young shoot-stop growing period) and October 23th (deciduous period). Soil PN and properties were determined, and the abundance of AOA and AOB was measured by real-time PCR using amoA gene copies. 【Results】 The highest contents of NO-3-N, available P and readily available K all appeared in April and those of NH+4-N in July, the lowest contents of NO-3-N, NH+4-N, available P and readily available K were in October in both orchard soils mostly. The pH of all soil samples was in the range from 4.25 to 6.09. The soil pH in D2 was significantly higher than in D1 in the same growth stages, while the NO-3-N and NH+4-N contents in D2 were lower than in D1 in different degrees. Soil samples collected in April had the highest PN rates and those collected in July had the lowest rates. Compared to D2, the PN values of D1 groups were significantly higher in April and October, while there were opposite results in July. Although the AOA and AOB abundances changed with the growth stages, the abundances of AOA were significantly higher than the abundances of AOB in all tested soils. In the same period, the AOA and AOB abundances of D2 soils were significantly higher than those of D1 soils, which might be related to soil pH. The correlation analysis showed that there were significant correlations between soil pH, NO-3-N and AOA and AOB, but the soil PN was only positively correlated with the AOA abundance.【Conclusions】 The long-term fertilization leads to low soil pH, which is an important factor affecting the abundances of AOA and AOB. The nitrification process in apple orchard soils is mainly related to AOA, and closely related to soil temperature and environmental factors. Fertilization and the returning of mowed weeds affect soil nitrogen contents and forms, slow down the acidification process of orchard soils.