The invention belongs to the technical field of bioengineering, and provides a PCR identification method for nitrifying bacteria. The PCR identification method for the nitrifying bacteria comprises the steps that a pair of specific primers are designed and synthesized with a specific characteristic gene-nitrite reductase gene (NiR) of the nitrifying bacteria as a template, the genomic DNA of the nitrifying bacteria is used as a template for PCR amplification, by optimizing the amplification conditions of PCR, agarose horizontal electrophoresis of PCR amplification products is carried out, andaccording to the presence and size of bands in an electrophoresis lane, whether bacterial strains belong to the nitrifying bacteria or not or whether mixed flora contains the nitrifying bacteria or not is judged. According to the PCR identification method for the nitrifying bacteria, the specific primers designed with the nitrate reductase gene as the template are PCR amplification primers, the experimental result specificity is high, the experimental operation is simple, the reliability of the results is high, an identification cycle of the nitrifying bacteria is shortened by optimizing PCR amplification conditions, the identification cycle is 45% shorter than conventional PCR amplification time, and a convenient and effective identification method is provided for the identification of anitrifying bacteria population.