Objective To investigate the expression of MDR1, CDR1, CDR2 and ERG11 genes in clinical fluconazole-resistant Candida albicans isolates, and explore its relationship with drug resistance. Methods The expression of drug resistance related genes MDR1, CDR1, CDR2 and ERG11 was detected by Real-Time PCR, and mean and standard deviation of △Ct in genes of susceptible strains were calculated, with lower than －3 s as overexpression. The efflux of Rhodamine6G was determined to examine the function of efflux pumps in the overexpression strains of Candida albicans. Results Among the 12 drug resistant strains, CDR1 and CDR2 were the most notable genes, with overexpression in 8 and 3 strains respectively. There was one strain overexpressing ERG11, and none for MDR1. The efflux of Rhodamine6G increased in the strains overexpressing efflux pumps, and the effect was enhanced after addition of glucose. As to the susceptible strains, there was almost no efflux before addition of glucose, and there was a slight change after addition of glucose. Conclusion Fluconazole-resistance is related to the overexpression of ABC transport protein superfamily, which is confirmed by the gene expression profile and function test of efflux pumps.