In Canada, the incidence of candidemia, the bloodstream infection caused by Candida species, varied from 1.2-5.1 cases/100,000, representing the third most common type of bloodstream infections in intensive care unit patients. However, the relative contributions of nosocomial transmission in candidemia remain poorly understood. In this study, we investigated the prevalence of nosocomial clusters among the causative agents for candidemia in Hamilton, Ontario, Canada, during a period from January 2005 to February 2009. We genotyped 134 isolates from 125 unrelated patients with candidemia, among which were 87 C. albicans, 20 C. parapsilosis, 11 C. glabrata, 15 C. tropicalis, and one C. krusei. Our PCR fingerprinting analyses using three highly polymorphic primers identified a total of 99 genotypes, with 18 of them shared by 44 independent isolates. Nine pairs of isolates were obtained from the same patients at the same time and each pair had identical fingerprints. Interestingly, all 44 independent strains belonging to each of the shared genotypes were isolated from patients within 3-months stay in the Hamilton hospitals. Both inter- and intra-ward clusters were found, including one that contained strains from intensive care units in two hospitals. Our results indicated that 33% of the patients with candidemia were infected by nosocomial clusters and suggested that measures should be taken in hospitals to prevent nosocomial acquisition of Candida infections.