Recent studies have clearly defined the vaginopathic Candida albicans strains that cause severe vulvovaginal candidiasis (VVC). Therefore, genotyping C. albicans isolates may predict the success of and assist in choosing the appropriate antifungal therapy. The purpose of this study was to compare the genotypes of C. albicans isolates causing VVC with those found in asymptomatic healthy pregnant and non-pregnant women in Adana, Turkey, as well as the antifungal susceptibility profiles of these isolates. A total of 216 independent C. albicans isolates were genotyped by allelic combination based on the microsatellite marker analysis of one such microsatellite, present in the promoter region of the elongation factor 3-encoding gene (CEF3) of C. albicans. The susceptibility testing profiles of all of the isolates against five antifungals and boric acid were obtained retrospectively from our laboratory records. We identified 20 genotypes on the basis of different allelic combinations at the CEF3 locus with a discriminatory power of 0.85. Genotypes 136-144 and 126-135 were present in 50 % of the isolates. No differences existed in the genotypic profiles of fungal isolates between pregnant and non-pregnant women. Remarkably, we did not find a single vaginopathic genotype. All of the isolates were susceptible to amphotericin B and 5-fluorocytosine, and the fluconazole and ketoconazole resistance rates were 0.9 and 3.7 %, respectively. Therefore, we did not find any correlation between genotype, severity of VVC, and antifungal resistance (P > 0.05). Even so, additional molecular data may provide new insights into the management of VVC.