We investigated the influence of long-term application of chemical fertilizer (NPK) and combined with wheat straw or livestock manures on the abundance of six nitrogen cycle genes (nifH, archaeal and bacterial amoA, nirS, nirK and nosZ) by quantitative PCR. Compared with non-fertilization treatment, long-term application of NPK fertilizers significantly increased the abundance of nirK, nosZ and bacterial amoA genes but decreased archaeal amoA gene abundance, with no significant effect on the abundance of nifH and nirS genes.