Vulvovaginal candidiasis (VVC), which is most frequently caused by Candida albicans, is a common problem worldwide. Despite the fact that extensive epidemiological studies have been performed, the cause of recurrent VVC (RVVC) remains uncertain. The aims of this work were to compare the genotypes of C. albicans strains causing different conditions of VVC, and explore the relationship between the drug resistance and genotype of C. albicans strains. In our study, we collected 649 independent strains from VVC patients in China. Isolates were tested for in vitro susceptibility to fluconazole, itraconazole, voriconazole, amphotericin B and caspofungin in accordance with the Clinical Laboratory Standards Institute (CLSI) document M27-A3. Genotyping was performed using PCR targeting specific CAI locus marker. C. albicans is the main pathogen of VVC, but the proportion of non-candida albicans (NAC) infection is also increasing, and we also found increased cases of mixed infection. Some C. albicans are resistant to multiple drugs. The strains with the genotypes including 16-16, 18-18 and 22-22 was likely to be the dominant genotype of uncomplicated VVC (p < 0.05). The genotypes of complicated VVC are mainly distributed in 30-45, 33-45, 32-46 and 39-45. Strains of 30-45, 32-45, 30-47 and 30-46 genotypes showed resistance to fluconazole, itraconazole, voriconazole and amphotericin B respectively. Our work suggests that the dominant genotypes with higher repeat number of C. albicans strains were more prevalent in patients with RVVC and drug-resistant strains, however, strains with uncomplicated VVC were more likely to distribute in homozygous. Identification of specific genotypes that correlate with different conditions of VVC and drug resistant is also of diagnostic and therapeutic significance.