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The global burden of HIV-associated cryptococcal meningitis (CM) is estimated at one million cases per year, causing up to a third of all AIDS-related deaths. Cryptococcus neoformans variety grubii (Cng) is the most ubiquitous cause of cryptococcal meningitis worldwide, however patterns of molecular diversity are understudied across some geographical regions experiencing significant burdens of disease. Cryptococcus species are notable in the degree that virulence differs amongst lineages, and highly virulent emerging lineages are changing patterns of human disease both temporally and spatially. Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied, yet increasingly important, group of pathogenic fungi. A multilocus sequence typing (MLST) scheme was used to characterise a genetically depauperate Cng population in Thailand, and a contrastingly highly diverse Cng population in Cape Town, South Africa. Sequence types (STs) from these populations were integrated into a dataset comprising global STs of Cng and patterns of range expansion were traced. Evidence from haplotypic networks and coalescent analyses revealed an ancestral African population of molecular type VNB, from which emerged a VNI lineage. This VNI lineage expanded globally out of Africa and led to the introduction of a limited number of genotypes in novel regions, including Asia. Bayesian inference estimated this spread of VNI to have occurred between 1 600 and 70 500 years ago, putatively vectored by the anthropogenically mediated spread of domesticated pigeons, historically native African birds. Clinical data collected from patients presenting with AIDS-associated CM showed that infecting African Cng isolates were associated with poorer long-term survival compared to Asian isolates. As mortality rates reported for these patients in Sub-Saharan Africa are higher than those seen in Asia, supported by a Galleria mellonella virulence model, this apparently elevated virulence is postulated as being the result of recombinant progeny with diverse phenotypes being created through frequent meiotic recombination.