- Elaeagnus, genus
- Elaeagnus mikii
- Elaeocarpus notoensis
- Elaphurus davidianus
- Elasmobranchii, class
- elata, Babylonia
- Elateridae, family
- Elatocladus, genus
- elegans, Lithophyllon
- elegans subsp. lobata, Podabacia
- elegans subsp. lobata forma vanderhorsti, Podabacia
- elegans, Minesedes
- elegans, Nododelphinula
- elegans, Paraleptolepis
- elegans, Podabacia
- elegans, Shurabia
- elegantissima, Alula
- elegantissima, Solenomorpha
- Elegant nutmeg
- elegantula, Pseudomelania
- elegantula, Turritella chichibuensis
- elegantula, Turritella (Hataiella)
- Elephant
- elephantoides, Stegodon
- Elephas, genus
- Elephas naumanni
- Eleutherococcus, genus
- Eleutherococcus sciadophylloides
- Elk
- Elliottia paniculata
- Ellipsonodosaria, genus
- elliptica, Cyclocardia
- elliptica, Lyonia ovalifolia
- elliptica, Siliqua
- elliptica, Venericardia
- Elm
- elongata, Acila
- elongata, Anadara amicula
- elongata, Arenomya grewingki
- elongata, Jolya
- elongata, Limopsis tokaiensis
- elongata, Mya grewingki
- elongata, Onychiopsis
- elongata, Panomya
- elongata, Thaumatopteris
- elongatus, Modiolus
- Elphidiella, genus
- Elphidium, genus
- Elphidium advenum
- Elphidium crispum
- Elphidium fax barbarense
- Elphidium fabum
- Elphidium hanzawai
- Elphidium subgranulosum
- Elphidium subincertum
- Enalaster nexilis
- Enallhelia, genus
- Enantiognathus, genus
- Enantiognathus ziegleri
- Encrinurus, genus
- Endemoconus oyamai
- Endictya robustus
- endoi, Equisetites
- endoi, Tetoria
- Endophycus wakinoensis
- Endophyllum, genus
- Endops yanagisawai
- Endothyra, genus
- Engraulidae, family
- Engraulis, genus
- Enida japonica
- Enkianthus campanulatus
- Ennucula, genus
- Ennucula akitana
- Ennucula cyrenoides
- Ennucula niponica
- Ennucula nipponica
- Ennucula tenuis
- Entada mioformosana
- Enteletes, genus
- Enteletes acutiplicatus
- Enteletes minoensis
- Enteletes suessi
- Entemnotrochus shikamai
- Entodesma navicula
- Entodesma naviculoides
- Entolium, genus
- Entolium inequivalve
- Entolium ussuricus
- Entomonotis, subgenus
- Entomonotis ochotica
- Entomonotis ochotica var. densistriata
- Entomonotis ochotica var. eurachis
- Erato, genus
- Ergalatax, genus
- Ericaceae, family
- ermanii, Betula
- Erman's birch
- erminea, Mustela
- Erodona, genus
- Erodona amurensis
- erosa, Carpinus
- erosa, Rhodopetoma
- Erosaria, genus
- erythrocomata, Chlamys islandica
- erythrocomatus, Pecten
- erythrodon, Corbula
- erythrodon, Solidicorbula
- Eubostrychoceras, genus
- Euclio, genus
- Euclio balantium
- Eucommia, genus
- Euconospira nipponica
- Eucrassatella nana
- Eucrassatella yabei
- Eucrate crenata
- Eucyrtidiellum, genus
- Eucyrtidiellum unumaense
- Eudolium nipponicum
- Euestheria, genus
- Euestheria kokurensis
- Eufenella pupoides
- euglypta, Cocconeis placentula
- euglypta, Leukoma
- euglypta, Protothaca
- Eumetopias, genus
- Eumetopias ojiyaensis
- Eumetopias sinanoensis
- Eumetopias watasei
- Eumorphotis, genus
- Eumorphotis multiformis
- Eunaticina, genus
- Eunotia, genus
- Euomphalus, genus
- Euomphalus asanoi
- Euomphalus (Straparollus), genus
- Euomphalus (Straparollus) asanoi
- Euonymus, genus
- Eupachydiscus haradai
- Eupecten ussuricus
- Euphyllia fimbriata
- Eupodiscus sculptus
- Eupsammia imperialis
- Euptelea, genus
- Euptelea polyandra
- eurachis, Entomonotis ochotica
- eurachis, Monotis ochotica
- Eurasian watermilfoil
- Eurhinodelphis, genus
- europaeus, Glyptostrobus
- Euroscaptor, genus
- Eurya, genus
- Eurya emarginata
- Euryale, genus
- eurypteron, Pteropurpura falcata
- eusculptum, Epitonium
- Eusilpha japonica
- Euspira, genus
- Euspira ashiyaensis
- Euspira meisensis
- Euspira pallida
- Euspira pila ovata
- Eutrephoceras japonicum
- ezoana, Cycadeoidea
- ezoana, Keteleeria
- ezoana, Monia macrochisma
- ezoana, Planera
- ezoana, Pterocarya
- ezoana, Woodwardia
- ezoanum, Acer
- ezoanus, Placunanomia macrochisma
- Ezocallista brevisiphonata
- ezoense, Equisetum
- eozensis, Inoceramus
- eozensis, Platyceramus
- ezonis, Nuttallia