Abstract: Objective To set up a duplex quantitative real-time PCR (QPCR) assay with high sensitivity, specificity and rapidity to detect Candida krusei and Candida glabrata. Methods A pair of species-specific primers, combined with two probes which were selected from the internally transcribed spacers Ⅱ (ITS Ⅱ), were used to amplify the common pathogen associated with the respiratory system in order to evaluate its sensitivity, specificity and repeatability. Results The results obtained from the duplex QPCR assay and the general culture were the same by detecting the samples of 100 cases. Its specificity was 100%,and its sensitivity was 100%. The lower limit of detection of this duplex QPCR assay was 10 copys of recombinant plasmid DNA. The result within group and between groups were the same as the general culture.Conclusion The duplex quantitative real-time PCR assay can detect Candida krusei and Candida glabrata sensitively, specifically, rapidly, simply and stably, and is useful to early diagnosis and target treatment of the diseases caused by the Candida.