The introduction of molecular techniques in the field of mycology had a dramatic impact on the classification of yeasts. In the early days of molecular mycology only a single locus was investigated, mostly a ribosomal DNA marker. During the past two decades, multi-gene phylogenies were used to have a better understanding of species complexes, this is in particular exemplified by the many studies on the Cryptococcus gattii/Cryptococcus neoformans species complexes. Until the 1980’s C. neoformans consisted of two varieties but due to the onset of the HIV-pandemic there was a sharp increase in cryptococcal infections, and forthcoming epidemiological studies that made use of molecular approaches described the presence of multiple genotypes. This led in 1999 to a minor taxonomic revision, namely to place serotype A and D isolates in the separate varieties grubii and neoformans, respectively. The third variety, gattii, that includes serotype B and C isolates was raised in 2002 to species level as C. gattii. In 2015 a taxonomic revision of the C. gattii/C. neoformans species complexes was proposed, this was driven by many molecular epidemiological studies that showed the presence of differences in genotypes and the occurrence of them in certain geographic areas and for specific environmental niches. Next to that there is increasing evidence that certain genotypes have a predilection to cause infection in specific hosts. Currently two species are recognized within the C. neoformans species complex and five within that of the C. gattii species complex. This taxonomic revision was made after more than 15 years of debate, and was driven by the ‘One Fungus = One Name’ principle, but till to date there is reluctance within the cryptococcal community to adopt the revised taxonomy. On the other hand, in the same year the taxonomy of basidiomycetous yeasts was largely revised, and the highly polyphyletic genus Cryptococcus was reduced from more than 100 species to only ten. The major pathogenic species remained in this genus, while other less clinically encountered species were placed into new genera. The taxonomic revision of the genus Cryptococcus has been adopted, and the same holds true for other important genera. For example, the members within the genus Trichosporon were accommodated into three genera. Molecular techniques have obviously led to an increase in species within medically important genera; a good example of that is the genus Malassezia that currently includes 17 species. Nowadays, the use of whole genome approaches has provided more evidence that several clinical relevant yeasts are in fact hybrids, which further complicates taxonomy.