The rising incidence of cryptococcosis, a life-threatening fungal infection affecting both immunocompromised and immunocompetent humans and animals, along with the emergence of outbreaks of infection, highlight the need of an increased and constant vigilance of its etiological agents Cryptococcus neoformans and C. gattii. The initial part of this PhD thesis evaluates MALDI-TOF MS and hyperbranched rolling circle PCR as two new alternative methodologies for the rapid and accurate identification of these two species and their major molecular types. The second part shows the utility of the insects Drosophila melanogaster and Galleria mellonella as invertebrate models of infection to study cryptococcal pathogenesis and virulence factors and to screen for strains with different levels of virulence. In the last part, different molecular approaches are applied to understand the epidemiology of cryptococcosis, and the differences regarding the genetic diversity, virulence and antifungal susceptibility between and within major molecular types/species. Being part of an ongoing research collaboration among different institutions, that continuously study the epidemiology, genetics and pathogenesis of these medically important yeasts, the population studies conducted during this PhD strongly contribute to our knowledge about the regional and global spread of Cryptococcus and the epidemiology of cryptococcosis.