Background: Candida albicans genotypes derived from PCR-based techniques targeting 25S rDNA have been shown to correlate with antifungal susceptibility and virulence factors. However, this method has not been used in isolates recovered from recurrent vulvovaginal candidiasis. Comparing intron-based genotypes with the drug susceptibility of isolates recovered from recurrent vulvovaginitis may aid in epidemiological studies and better patient management. Objectives: The purpose of this study was to investigate the genetic diversity of isolates involved in vulvovaginal candidiasis and their susceptibility to seven antifungal agents. Methods: Candida genotyping based on the presence or absence of a group I intron by PCR targeting 25S rDNA and drug susceptibility assays using a modified Alamar Blue broth microdilution method were carried out. Fisher's exact test and the Mann-Whitney U test were performed, and P < 0.05 was considered statistically significant. Results: Candida albicans was the predominant species among 384 Candida isolates followed by C. glabrata in acute and C. tropicalis in recurrent vulvovaginitis. Candida albicans from acute infections were more susceptible to fluconazole than isolates from recurrent cases but more resistant to miconazole and amphotericin B. The dominant genotype A was resistant to itraconazole and demonstrated higher minimal inhibitory concentrations (MICs) to 5-fluorocytosine and itraconazole. All C. albicans and nonalbicans species. with the group I intron were susceptible to 5-fluorocytosine. Conclusions: Candida albicans is the predominant cause of acute and recurrent vulvovaginal candidiasis, and drug susceptibility differed significantly among type of infection. Strain differences based on the group I intron may not be clinically significant in disease recurrence. However, the presence or absence of the group I intron has significant impact on antifungal MICs and resistance. Moreover, the group I intron in C. albicans and non-albicans may be the most important factor related to 5-fluorocytosine susceptibility.