Wickerhamomyces anomalus,previously known asCandida pelliculosa,occasionally causes candidemia in humans, primarily infecting neonates, and infants. The mortality rate of these invasive infections is high, and isolates with a reduced susceptibility to fluconazole have been reported.W. anomalusoutbreaks are regularly reported in healthcare facilities, especially in neonatal intensive care units (NICUs). In order to rapidly genotype isolates with a high-resolution, we developed and applied a short tandem repeat (STR) typing scheme forW. anomalus. Six STR markers were selected and amplified in two multiplex PCRs, M3 and M6, respectively. In total, 90W. anomalusisolates were typed, leading to the identification of 38 different genotypes. Four large clusters were found, unveiling simultaneous outbreak events spread across multiple units within the same hospital. STR typing results of 11 isolates were compared to whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) calling, and the identified genotypic relationships were highly concordant. We performed antifungal susceptibility testing of these isolates, and a reduced susceptibility to fluconazole was found for two (2.3%) isolates.ERG11genes of these two isolates were examined using WGS data, which revealed a novel I469L substitution in one isolate. By constructing a homology model forW. anomalus ERG11p, the substitution was found in close proximity to the fluconazole binding site. In summary, we showed multipleW. anomalusoutbreak events by applying a novel STR genotyping scheme.