OBJECTIVES: Fluconazole, alone or in association, is often administered during cryptococcal meningitis treatment, especially in sub-Saharan Africa. Its extensive use has led to the emergence of resistant strains. The mechanisms underlying resistance are poorly documented for yeasts belonging to the Cryptococcus gattii species complex. The literature suggests that this resistance could be due to mutations and/or overexpression of the ERG11 gene (encoding the 14-α-demethylase) and efflux pumps, such as MDR (a sub-class of ABC transporters) or AFR (a second sub-class of ABC transporters). We highlight the presence of genotype VGII strains (C. deuterogattii) from the Ivory Coast with a rare sequence type 173, that are associated with high minimum inhibitory concentrations of FCZ compared to those for strains originating from the Pacific Northwest (USA). METHODS: We investigated the mechanisms of fluconazole resistance in 28 Ivorian clinical C. deuterogattii strains recovered from 3 patients during their follow-up and antifungal treatment. RESULTS: We demonstrated that (i) these strains exhibited no mutation in the ERG11 gene; (ii) some strains had increased ERG11 and MDR1 mRNA expression, while AFR1 and AFR2 were not overexpressed in strains with high MICs of FCZ compared with the expression levels for strains with low MICs of FCZ; and (iii) exposure to FCZ in strains with high MICs of FCZ induced AFR1 mRNA overexpression. CONCLUSION: We demonstrated that the FCZ-resistant mechanism commonly described in C. neoformans was not responsible for the resistance to FCZ in the rare subtype strains.