- Ebala Gray 1847
- Ebaliopsis Ihle 1918
- Echelus Rafinesque 1810
- Echeneibothrium Van Beneden 1849
- Echeneis Linnaeus 1758
- Echinochloa P. de Beauvois
- Echinococcus Rudolphi 1801
- Echinolampas Gray 1825
- Echinolittorina Habe 1956
- Echinoparyphium Dietz 1909
- Echinopla Smith 1857
- Echinopora Lamarck 1816
- Echinostoma Rudolphi 1809
- Echinuria Soloviev 1912
- Echynotriton Nussbaum & Brodie 1982
- Ecklonia Hornemann 1828
- Ecsenius McCulloch 1923
- Ectocyclops Brady 1904
- Ectomomyrmex Mayr 1867
- Ectopleura L. Agassiz 1862
- Egeria Planchon
- Egretta T. Forster 1817
- Eguchipsammia Cairns 1994
- Ehretia P.Browne
- Eimeria Schneider 1875
- Eisenia J.E. Areschoug 1876 (Phaeophyceae)
- Eisenia Michaelsen 1900 (Oligochaeta)
- Elaeagnus Linné
- Elaeocarpus Linné 1760
- Elagatis Bennett 1840
- Elaphe Wagler 1833
- Elaphoidella Chappuis 1928
- Elaphrus Fabricius 1775
- Elaphropus Motschulsky 1839
- Elasmopus A. Costa 1853
- Eleginus G. Fischer 1813
- Eleotris Gronovius 1763
- Eleusine J. Gaertner
- Eleutherococcus Maximovich 1855
- Eleutheronema Bleeker 1862
- Ellobius Fischer 1814
- Elthusa Schioedte & Meinert 1884
- Emberiza Linnaeus 1758
- Emmelichthys Richardson 1845
- Encrasicholina Fowler 1938
- Endasys Förster 1869
- Endochus Stål 1859
- Engraulis Cuvier 1816
- Engyprosopon Günther 1862
- Enispa Schioedte & Meinert 1884
- Enneapterygius Rüppell 1835
- Enochrus Thomson 1859
- Entacmaea Ehrenberg 1834
- Enterobius Leach 1853
- Enteromorpha Link 1820
- Entomacrodus Gill 1859
- Entosiphon Stein 1878
- Entosphenus T.N. Gill 1862
- Eohaustorioides Bousfield in Bousfield & Tzvetkova 1982
- Eolagurus Argyropulo 1946
- Eophona Gould 1851
- Eopsetta Jordan & Goss 1885
- Eothenomys Miller 1896
- Epactophanes Mrázek 1893
- Ephialtes Gravenhorst 1829
- Epidamaeus Bulanova-Zachvatkina 1957
- Epilachna Chevrolat in Dejean 1836
- Epinephelus Bloch 1793
- Epiphanes Ehrenberg 1832
- Epipremnum H.W. Schott 1857
- Epitheca Burmeister 1839
- Epitonium Röding 1798
- Epizoanthus Gray 1867
- Eplumula Williams 1982
- Epomidostomum Skrjabin 1915
- Epomis Bonelli 1810
- Eptatretus Cloquet 1819
- Equisetum Linné
- Equulites Fowler 1904
- Eragrostis Wolf
- Eretes Laporte 1833
- Ergalatax Iredale 1931
- Ergasilus von Nordmann 1832
- Erinaceusyllis San Martín 2005
- Eriobotrya Lindley
- Eriocheir De Haan 1835
- Eriotremex Benson 1943
- Eriphia Latreille 1817
- Erisphex D.S. Jordan & Starks 1904
- Erithacus Cuvier 1800
- Ernestinus Distant 1911
- Erosa Swainson 1839
- Erythrocles Jordan 1919
- Esox Linnaeus 1758
- Esperiopsis Carter 1882
- Etrumeus Bleeker 1853
- Eualus Thallwitz 1892
- Eucalanus Dana 1852
- Eucalathis Fischer & Œhlert 1890
- Eucheilota McCrady 1859
- Euchelipluma Topsent 1909
- Euchlanis Ehrenberg 1832
- Euchone Malmgren 1866
- Euchoreutes Sclater 1891
- Eucoila Westwood 1833
- Eucoilia Westwood 1839
- Eucoleus Dujardin 1845
- Eucyclops Claus 1893
- Eudendrium Ehrenberg 1834
- Eufilaria Seurat 1921
- Eugenuris Schulz 1948
- Euglena Ehrenberg 1830
- Eugnathogobius Smith 1931
- Eugymnanthea Palombi 1936
- Euhadra Pilsbry 1890
- Eulaelaps Berlese 1903
- Eulalia Savigny 1817
- Eulamia Gill 1862
- Eumecichthys Regan 1907
- Eumerus Meigen 1822
- Eumetopias Gill 1866
- Eumida Malmgren 1865
- Eunice Cuvier 1817
- Eupatorium Linné
- Euphaedusa Böttger 1877
- Euphausia Dana 1850
- Euphorbia Linné
- Euphyllia Dana 1846
- Euphysora Maas 1905
- Euplectella Owen 1841
- Euplica Dall 1889
- Euplynes Schmidt-Goebel 1846
- Euponera Forel 1891
- Euraphia Conrad 1837
- Eurema Hübner 1819
- Eurhamphaea Gegenbaur 1856
- Euroscaptor Miller 1940
- Eurya Thunberg 1783
- Euryale R.A. Salisbury
- Eurycea Rafinesque 1822
- Euryperis Motschulsky 1850
- Eurythenes Smith 1882
- Eurythoe Kinberg 1857
- Eurythoracana E. Strand 1936
- Eurytoma Illiger 1807
- Eusilpha A.P. Semenov 1890
- Eusphingonotus Bey-Bienko 1950
- Eusphyra T.N. Gill 1862
- Eustomias Filhol 1884
- Eustrongylides Jägerskiöld 1909
- Eutaeniichthys Jordan & Snyder 1901
- Eutamias Trouessart 1880
- Euthynnus Lütken in Jordan & Gilbert 1883
- Eutima McCrady 1859
- Eutomostethus Enslin 1914
- Eviota Jenkins 1903
- Evynnis Jordan & Thompson 1912
- Excirolana Richardson 1912
- Exogone Örsted 1845
- Exorchis Kobayashi 1921