Thirty strains of seven Candida species from CICC(China Center of Industrial Culture Collection)were studied. The strains were differentiated by ITS1 region PCR-SSCP fingerprinting analysis and ITS2 region PCR-SSCP fingerprinting analysis. Results showed that both ITS1 region and ITS2 region were able to differentiate the seven species of Candida clearly. Contrasting the maps and effects on the identification of Candida species of ITS1 region with that of ITS2 region, result indicated that on the identification of Candida species the application of ITS2 region was better than ITS1 region.