| Zygosaccharomyces ashbyi Cordroch synonym of: Kluyveromyces marxianus (E.C. Hansen) Van der Walt |
| Zygosaccharomyces bailii (Lindner) Guilliermond var. bailii |
| Zygosaccharomyces bisporus H. Naganishi |
| Zygosaccharomyces chevalieri (Guilliermond) Klöcker var. fermentati Saito synonym of: Pichia manshurica Saito |
| Zygosaccharomyces chevalieri Guilliermond synonym of: Pichia manshurica Saito |
| Zygosaccharomyces cidri (Legakis) Yarrow synonym of: Lachancea cidri (Legakis) Yarrow |
| Zygosaccharomyces favi Péter, Čadeż & Dlauchy |
| Zygosaccharomyces fermentati H. Naganishi synonym of: Lachancea fermentati (Naganishi) Kurtzman |
| Zygosaccharomyces florentinus Castelli ex Kudryavtsev synonym of: Zygotorulaspora florentina (T. Castelli ex Kudryavtsev) Kurtzman |
| Zygosaccharomyces gambellarensis Torriani, Lorenzini, Salvetti & Felis |
| Zygosaccharomyces gracilis subsp. italicus Sacchetti synonym of: Zygosaccharomyces rouxii (Boutroux) Yarrow |
| Zygosaccharomyces mellis Fabian & Quinet |
| Zygosaccharomyces microellipsoides (Osterwalder) Yarrow synonym of: Torulaspora microellipsoides (Osterwalder) Van der Walt & Johannsen |
| Zygosaccharomyces mrakii Capriotti synonym of: Zygotorulaspora mrakii (Capriotti) Kurtzman |
| Zygosaccharomyces parabailii S.O. Suh, Gujjari, Beres, B. Beck & J.J. Zhou |
| Zygosaccharomyces pastoris Guilliermond synonym of: Komagataella pastoris (Guilliermond) Yamada et al. |
| Zygosaccharomyces pini Holst synonym of: Ogataea pini (Holst) Y. Yamada, M. Matsuda, K. Maeda & Mikata |
| Zygosaccharomyces rouxii (Boutroux) Yarrow |
| Zygosaccharomyces sapae Solieri, Chand Dakal & Giudici |
| Zygosaccharomyces siamensis Saksinchai, M. Suzuki, Chantawannakul, Ohkuma & Lumyong |
