Nine methanol-assimilating yeast strains isolated from olive oil sediments in Slovenia, extra virgin olive oil from Italy and rotten wood collected in Hungary were found to form three genetically separated groups, distinct from the currently recognized yeast species. Sequence analysis from genes of the small subunit (SSU) rRNA, internal transcribed spacer region/5.8S rRNA, large subunit (LSU) rRNA D1/D2 domains and translational elongation factor-1α (EF-1α) revealed that the three closely related groups represent three different undescribed yeast species. Sequence analysis of the LSU rRNA gene D1/D2 domains placed the novel species in the Ogataea clade. The three novel species are designated as Ogataea kolombanensis sp. nov. (type strain: ZIM 2322(T) = CBS 12778(T) = NRRL Y-63657(T)), Ogataea histrianica sp. nov. (type strain: ZIM 2463(T) = CBS 12779(T) = NRRL Y-63658(T)) and Ogataea deakii sp. nov. (type strain: NCAIM Y.01896(T) = CBS 12735(T) = NRRL Y-63656(T)).