Cryptococcus neoformans is a species complex of often highly pathogenic fungi that cause significant disease in humans. Cryptococcus is notable in the degree that virulence differs amongst genotypes, and highly-virulent emerging lineages are changing patterns of disease in time and space. Cryptococcus neoformans variety grubii (Cng) causes meningitis among HIV/AIDS patients, up to 1 million cases/year resulting in over 600,000 mortalities. Despite these rates of mortality being comparable to those caused by malaria (one million mortalities per annum), cryptococcal meningitis receives only a fraction of the attention, funding and control granted to more widely recognised diseases. This study uses multilocus sequence typing to compare the genetic diversity of Cng in a largely unstudied country with an emerging HIV epidemic, Thailand, against the diversity seen elsewhere. We found that Cng in Thailand exhibits significantly less genetic diversity in comparison to other areas of the world, especially Africa. Analyses dating the pathogen's origin in Thailand support the introduction of a limited number of genotypes into Southeast Asia from an ancestral African population within the last 7,000 years. These findings show the power associated with the collection of global sequence databases in order to better understand the evolution of major fungal pathogens.