Members of Cryptococcus neoformans (C.n. ) species complex cause life-threatening infections. Its taxonomy is an open question, with 2 anamorph species originally described: C. neoformans & C. gattii. Mating experiments linked them to the teleomorph genus Filobasidiella, establishing 2 varieties: C.n. var. neoformans = F.n. var. neoformans (serotypes A, D & AD) & C.n. var. gattii = F.n. var. bacillispora (serotypes B & C). C.n. var. grubii, was established as a separate variety causing most infections. Molecular data suggested C.n. var. gattii as a new species, C. bacillisporus, recently renamed as C. gattii. PCR-fingerprinting, AFLP, URA5, PLB1 & ACT1 RFLP analysis, sequencing (ITS, URA5, PLB1 & ACT1) & microsatellite analysis have been used to study the genetic diversity of the C.n. species complex. PCR-fingerprinting, AFLP & RFLP analysis divided more than 1000 global isolates into 8 molecular types. VNI/AFLP1 & VNII/AFLP1A = C.n. var. grubii, serotype A; VNIII/AFLP3 = hybrid between C.n. var. grubii & C.n. var. neoformans, serotype AD; VNIV/AFLP2 = C.n. var. neoformans, serotype D; & VGI/AFLP4, VGII/AFLP6, VGIII/AFLP5 & VGIV/AFLP7 = C. gattii, serotypes B & C. AD hybrid isolates (VNIII/AFLP3) revealed patterns that correspond to a number of molecular types, suggesting recombination events leading to diploid or aneuploid strains. VNI & VGI are the predominant genotypes worldwide. Similar regional profiles of tree-derived & clinical isolates support an epidemiological link. The Vancouver Island outbreak is caused by the rare genotype VGII/AFLP6, which seems to be emerging in temperate climates (Greece & Colombia). Whole genome sequence analysis of the strains H99 (C.n. var. grubii ), B3501 & JEC21 (C.n. var. neoformans ) & WM276 (C. gattii ) has shown different levels of microsatellite abundance & polymorphism per variety/species & large variations in the flanking regions. The genotypic variation found among the 8 molecular types lies within a comparable range of that found in established fungal species, suggesting further speciation of the C.n. species complex. The specificity of the microsatellite flanking regions to a certain genotype is adding evidence to the existence of separate species.