Members of the Cryptococcus neoformans/C. gattii species complex are grouped into eight molecular types, differing in their epidemiology, disease severity and geographic range. Recent in vitro antifungal susceptibility studies of isolates of the complex revealed contradictory results. The objective of the present study was to assess if this variation is random or correlates with different molecular types by testing the in vitro antifungal susceptibility of 18 C. neoformans (VNI), 11 C. gattii (VGI) and 38 C. gattii (VGII) strains from Brazil to eight antifungal drugs using the CLSI microdilution method. We herein report that the molecular type VGII is the least susceptible genotype, followed by VGI and VNI. This indicates a clear correlation between antifungal susceptibilities and genotypes of the causative cryptococcosis agents, emphasizing the importance of determining the molecular type as part of the clinical diagnostic process to enable an informed decision as to the most appropriate antifungal treatment.