• Eugenia Gould, 1855 (unaccepted > nomen nudum) [Family: Aves (awaiting allocation)]
• Eugenia Gould, 1856 (uncertain) [Family: Aves (awaiting allocation)]
• Eugenia Hall, 1867 accepted as Engina Gray, 1839 [Family: Buccinidae]
• Eugenia Iljin, 1930 (uncertain) [Family: Cnidaria (awaiting allocation)]
• Eugenia Linnaeus, 1753 [Family: Myrtaceae]
• Eugenia Martens, 1860 (uncertain) [Family: Mollusca (awaiting allocation)]
• Eugenia Robineau-Desvoidy, 1863 (accepted > junior homonym) [Family: Tachinidae]
• Eugenia Savchenko, 1977 accepted as Savchenkoiana Koçak, 1981 [Family: Pediciidae]
• Eugenia binacag Elmer accepted as Eucalyptus deglupta Bl.
• Eugenia fugax Robineau-Desvoidy, 1863
• Eugeniacrinites Miller, 1821 †
• Eugeniacrinitidae Roemer, 1855 †
• Eugeniacrinus Agassiz, 1836 (uncertain)
• Eugeniaites A. Loubière, 1933 † (unaccepted)
• Eugeniaïtes A. Loubière, 1933 † represented as Eugeniaites A. Loubière, 1933 †
• Eugeniamyia Maia, Mendonca & Romanowski, 1997 accepted as Maiamyia Evenhuis, 2022 [Family: Cecidomyiidae]
• Eugeniamyia Williston, 1882 accepted as Hammerschmidtia Schummel, 1834 [Family: Syrphidae]
• Eugeniamyia dispar Maia, Mendonca & Romanowski, 1997
• Eugeniana Narayanan, Subba Rao & Patel, 1958 accepted as Anselmella Girault, 1926