The yeasts Candida krusei and Candida inconspicua have similar phenotypes, which may make discrimination of these organisms difficult. In this study we determined the karyotypes of 51 isolates of these two yeast species by contour-clamped homogeneous electric field electrophoresis. We found that the 43 isolates that had the C. krusei phenotype had three karyotype-specific characteristics. These isolates produced either two or three bands between 2,000 and 3,000 kb and no band between 1,300 and 2,000 kb, and there was either a single bright band at 1,300 or 1,200 kb or two separate bands at 1,300, 1,200, or 1,100 kb. Using this technique, we were able to distinguish 27 different C. krusei types on the basis of band variations. The seven isolates identified as C. inconspicua on the basis of phenotype differed in that they produced at least one band between 1,300 and 2,000 kb. These isolates produced six to nine bands, in contrast to C. krusei strains, which produced three to six bands. The MIC of fluconazole for all of the isolates was at least 12.5 mg/liter, as determined by a broth dilution method.