Candida krusei is inherently resistant to fluconazole and is an important pathogen responsible for nosocomial candidiasis especially in patients with hematological malignancy. Despite the growing clinical importance of C.krusei infections, little is known of its genetic diversity and molecular epidemiology. Therefore, differentiating between C.krusei isolates is of importance for a better understanding of the epidemiology, mode of transmission and pathogenesis of the organism. We investigated the use of two different methods (restriction endonuclease analysis of genomic DNA (REAC) with Hinfl and polymerase chain reaction by using Arno1 and Arno2 primers) for molecular typing of 56 C.krusei isolates from 56 patients. Ten different types (A-J) were determined by REAG. Depending on the patterns of isolates, the number of the bands varied from 12 to 15 and the size of the fragments varied from 2.0 kb to 6.2 kb. Of the isolates 71.4% were gathered under three major patterns (D, F, H). In the second method, PCR amplified different sizes of fragments varied approximately from 1 kb to 2 kb, which yielded 13 types (a-m) from 56 patients. Four major patterns (d, f, h, k) were observed for 58.9% of the isolates. The genotypes detected by REAG and PCR methods were found to be same in 43 isolates out of 56. As the banding patterns of the isolates were found to be similar in this study, it was thought that an exogenous origin could be the source of infections caused by C.krusei isolates. Both REA of genomic DNA and PCR analysis seem to be useful for the typing of C.krusei, however PCR assay can be preferred as it is a simple and rapid method. As a result, further studies are required for the validation of reproducibility and discriminatory power of these methods.