To identify the 16S?23S rRNA gene in Klebsiella pneumoniae, a PCR-DHPLC assay was performed in this study. Primers specific for the 16S?23S rRNA gene of Klebsiella pneumoniae in diary were selected to conduct the DHPLC assays. The specific testing was performed with Klebsiella pneumoniae and 57 strains, and various grads of Klebsiella pneumoniae was used for the sensitivity testing. The good specificity was found in this study. Also, the method showed nice sensitivity with the lowest amount of detecting at 100 CFU/mL, so it can detect and identify Klebsiella pneumoniae quickly and correctly. The DHPLC could be a new method for detecting diary pathogens.