The systematic of ascomycetous yeasts has traditionally relied on phenotypic characters, some of which have been recognised to be subject to convergent evolution and intraspecies variation. As a result, most genera are polyphyletic and should be considered as informal groupings to aid in communication. A stable and informative classification should be based on natural relationships. The inference of those, especially in the artificial genus Candida, relies almost exclusively on the phylogenies of genes. To date, molecular phylogeny of yeasts is mainly based on genes of the ribosomal gene cluster. This study compares phylogenies resulting from the actin gene, the small and large subunit ribosomal RNA genes of ascomycetous yeasts. As the gene phylogenies were only partially congruent, the evolutionary history of the genes was investigated and independent markers of high evolutionary stability were mapped onto the gene trees to confirm or reject phylogenetic hypotheses.
