We describe a whole genome sequencing (WGS) investigation that was initiated following concerns raised by the infectious disease consultation service and antimicrobial stewardship teams about an increasing number of fluconazole (FLU) non-susceptible C. parapsilosis clinical isolates identified within two acute care hospital networks in Ontario that are in close geographic proximity. We show the utility of phylogenomic analysis in identifying the cause of the increased number of FLU non-susceptible C. parapsilosis clinical isolates, distinguishing between alternate hypotheses of an outbreak due to horizontal transmission of FLU non-susceptible C. parapsilosis or multiple independent evolutions of FLU resistance as a result of antimicrobial selection pressure. Furthermore, we show that WGS analysis has the added benefit of enabling interrogation of genomes for potential genetic causes of antifungal resistance.