The molecular epidemiology and the antifungal susceptibility profiles of Candida albicans are scarce in Cameroon. Authors studied the genetic diversity and the antifungal susceptibility of C. albicans isolates from Yaoundé HIV-infected patients. Clinical isolates were obtained by mycological diagnosis of oropharyngeal swabs, stools, urine, and vaginal swabs from patients. C. albicans isolates were confirmed by the Light cycler real-time PCR of the ITS1 region of the 5.8s ribosomal DNA. The ABC genotypes and the Hwp1 gene amplification were carried out with specific primers. Microsatellite length polymorphism of HIS3, CDC3, and EF3 microsatellites was analysed. The antifungal susceptibility testing was carried out by the CLSI broth microdilution M27-A3 and M27-S4 protocols. The minimal inhibitory concentration (MIC) results were interpreted according to updated clinical breakpoints (CBPs) recommended by the CLSI or epidemiological cut-off values (ECVs). One hundred and thirteen (113) isolates were obtained from the analysis of 1218 samples. The ABC genotyping showed 79 (69.91%) genotype A, 24 (21.23%) genotype B, and 10 (8.84%) genotype C. The Hwp1 gene amplification provided a newly observed genetic polymorphism, named H and 5 genotypes described (H1-H5). The microsatellite analysis generated 65 molecular types. All the isolates were susceptible to amphotericin B (MIC ≤ 1 μg/ml); 79.64% of isolates were wild type to itraconazole (MIC ≤ 0.12 μg/ml); and 86.72% of isolates were susceptible to fluconazole (MIC ≤ 2 μg/ml). These results highlight the important genetic diversity of C. albicans isolates among Yaoundé HIV-infected patients and bring clues for the comprehension of the molecular epidemiology of the yeast in Cameroon.