This article discusses the population heterogeneity in Cryptococcus neoformans and its impact on pathogenesis. Cryptococcus neoformans is a prevalent global threat, especially for people living with HIV. The article explores the different ways in which the human-Cryptococcus interaction can progress, including latent/dormant cryptococcosis, pulmonary cryptococcosis, disseminated cryptococcosis, and cryptococcal relapse. The article also examines population heterogeneity in C. neoformans, which provides benefits to the pathogen in coping with changing conditions and contributes to its survival. The specific manifestations of population heterogeneity discussed in the article include heteroresistance, viable but nonculturable state, antifungal persistence, and biofilm formation. The article highlights the influence of population heterogeneity on the survival and pathogenesis of C. neoformans.