Aims: This study was conducted to determine the respective prevalence of Candida species and to study their sensitivity profile to antifungal agents to identify the emergence of resistance.Methods: This retrospective study was conducted from 2017 to 2019 at the Institute Pasteur of Côte d’Ivoire on patients with fungal disease. Various samples were analysed first by conventional methods. Then, the results were confirmed by MALDI-TOF-MS. Sensitivity tests were performed using the CLSI method and evaluated by the M59 benchmark.Results: In total, 227 Candida species were isolated from 1966 patients. Most of the samples were vaginal swabs (120/228). Using the conventional method, C. albicans was prevalent, being present in 52.6% of the samples. There were mixtures of 2 to 4 species in 36.8% of the samples that were not identified at the first identification. Confirmation by MALDI-TOF-MS showed a 35.18% prevalence of C. tropicalis. Thirteen species were identified, and 2 species complexes (C. albicans and C. parapsilosis) were highlighted in a final cohort of 315 Candida strains.Conclusion: This study highlights the difficulty of correct identification in developing countries. The transition from standard identification to molecular biology is essential and must be considered for improvement in public health.