Relationships among species assigned to the yeast genera Pichia, Issatchenkia and Williopsis, which are characterized by the ubiquinone CoQ-7 and inability to utilize methanol, were phylogenetically analyzed from nucleotide sequence divergence in the genes coding for large and small subunit rRNAs and for translation elongation factor-1α. From this analysis, the species separated into five clades. Species of Issatchenkia are members of the Pichia membranifaciens clade and are proposed for transfer to Pichia. Pichia dryadoides and Pichia quercuum are basal members of the genus Starmera. Williopsis species are dispersed among hat-spored taxa in each of the remaining three clades, which are proposed as the new genera Barnettozyma, Lindnera and Wickerhamomyces. Lineages previously classified as varieties of Pichia kluyveri, ‘Issatchenkia’scutulata, Starmera amethionina and ‘Williopsis’saturnus are elevated to species rank based on sequence comparisons.