The present investigation aimed to assess the prevalence of genotypes of C. albicans in Ouagadougou and to analyze the relationship between the genetic diversity and antifungal susceptibility. Ninety-six clinical strains are included. They were diagnosed as C. albicans using germ tube test, chlamydospore formation, and Api-Candida test. Genotyping was performed using PCR targeting 25S rDNA. Antifungal susceptibilities were tested based on the disk diffusion method. The genotypes A (85.4%) was predominant followed by genotypes B (10.4%) and C (4.2%). The highest resistance rate with genotype A was obtained with fluconazole (74.4%). A resistance to amphotericin B was observed with genotypes A (29.3%) and B (30%).