- Dactylioceras helianthoides
- Dadoxylon, genus
- Dadoxylon japonicum
- Dahurian birch
- Dahurian larch
- dahurica, Betula
- daijimaensis, Ilex
- Daimyo oak
- Daira, genus
- daishakaensis, Chlamys
- daitokudoensis, Anadara
- Dalatias, genus
- dalli, Acharax
- Dallina miyatokoensis
- dalli obliquata, Pseudogramatodon
- dalli, Porterius
- dalli, Pseudogramatodon
- dalli, Solemya
- Damesites, genus
- Danubites japonicus
- Daonella, genus
- Daonella kotoi
- daphnoides, Cinnamomum
- Dark-winged fungus gnat
- Dasyatidae, family
- Dasyatis‘®
- Dasyatis nipponensis
- datensis, Cibicides
- Davallia, genus
- Davallia mariesii
- davidiana var. japonica, Ulmus
- davidiana, Keteleeria
- davidianus, Elaphurus
- davurica, Betula
- Decapod
- Decapoda, order
- Decapodiformes, superorder
- Decatopecten, genus
- Decatopecten izuensis
- declivis biconica, Siphonalia
- declivis, Siphonalia
- declivis, Suavodrillia
- decora, Belleza
- decoratum, Clinocardium
- decoratus, Spondylus
- Decorifer, genus
- Decorifer matusimanus
- decurrens, Woodwardia
- decussata, Crenella
- decussatoides, Tugali
- Deep sea scallop
- Deerfoot fern
- degronianum, Rhododendron
- dehiscens, Sphaeroidinella
- Delectopecten macrocheiricola
- Delectopecten peckhami
- Delectopecten vancouverensis
- delicata, Neoschwagerina
- delicata, Stromatopora
- delicatula, Ctena
- Delphinidae, family
- Deltocyathoides orientalis
- demersum, Ceratophyllum
- Dendostrea paulucciae
- Dendostrea rosacea
- Dendrophyllia, genus
- Dendroxena sexcarinata
- denselamellosa, Ostrea
- denselineata, Nassa
- denselineatus, Nassarius
- denseplicatum, Gaudryceras
- densicingulata, Shikamainosorex
- densicostata, Acrilla
- densicostata, Amaea
- densiflora, Pinus
- densinervis, Nilssonia
- densistriata, Entomonotis ochotica
- densistriata, Monotis ochotica
- Dentalina, genus
- Dentalina setanaensis
- Dentalium, genus
- Dentalium akasakensis
- Dentalium buccinulum
- Dentalium (Fissidentalium) watanabei
- Dentalium hexagonum
- Dentalium neornatum
- Dentalium octangulatum
- Dentalium octangulatum hexagonum
- Dentalium rhabdotum
- Dentalium septentrionale
- Dentalium watanabei
- Dentalium weinkauffi
- Dentalium yokoyamai
- dentata, Hausmannia
- dentata, Quercus
- Denticula, genus
- Denticula hustedtii
- denticulata, Cladophlebis
- Denticulopsis, genus
- Denticulopsis hustedtii
- Denticulopsis praedimorpha
- dentiformis, Premocyathus
- Dentoglobigerina globosa
- depressa, Protorotella
- depressa, Vaginella
- Derjuginella, genus
- Deroceras, genus
- Desmoceras japonicum
- Desmoceras (Pseudouhligella) japonicum
- Desmostylus, genus
- Desmostylus japonicus
- desori, Isurus
- Deutzia crenata
- dewana, Dusisiren
- deweveri, Dictyomitrella
- deweveri, Triassocampe
- diabolicum, Acer
- Diacria trispinosa
- Diacrolinia aurita
- dianae, Leucotina
- Diaphus, genus
- Diartus hughesi
- Diatoma vulgare var. linearis
- Diatoma vulgaris var. linearis
- Diatom, class
- Dibunophyllum, genus
- Dicerorhinus nipponicus
- Dicrocerus tokunagai
- Dictyocha speculum
- Dictyochophyceae, class
- Dictyomitra koslovae
- Dictyomitrella, genus
- Dictyomitrella deweveri
- Dictyophyllum, genus
- Dictyophyllum falcatum
- Dictyophyllum japonicum
- Dictyozamites kawasakii
- Dictyozamites reniformis
- Didimacar tenebrica
- didyma coticazae, Glossaulax
- didyma coticazae, Neverita
- didyma, Glossaulax
- didyma, Neverita
- Didymoceras, genus
- Didymoceras awajiense
- Didymoceras nakaminatoense
- dielsiana, Stephania
- difficilis, Modiolus modiolus
- difficilis, Volsella
- digitata, Ginkgoites
- digitata var. huttoni, Ginkgoites
- dilatata, Barnea
- dilatatum, Rhododendron
- dilatatum, Viburnum
- dilatoseptatum, Tipheophyllum
- diluvianum, Lopha
- diluvianum, Rastellum
- diminuta, Cocconeis
- diminuta, Pinnularia brebissonii
- Dineutus australis
- Dineutus orientalis
- Dinocardium braunsi
- Dinoflagellata, phylum
- Dinoflagellate
- Dinosaur
- Dinosauria, superorder
- Diodora, genus
- Diodora mus
- Diodora quadriradiata
- Diodora yokoyamai
- Diodora yokoyamai koshibensis
- Diodora yokoyamai kosibensis
- dioicus var. kamtschaticus, Aruncus
- Dioon, genus
- Diospyros, genus
- Diospyros miokaki
- Diplazontinae, subfamily
- Diplodonta (Felaniella) usta
- Diplodonta ferruginata
- Diplodonta semiasperoides
- Diplodonta usta
- Diplomoceras, genus
- Diplomystus altisomus
- Diplomystus kokuraensis
- Diplomystus primotinus
- Diploneis, genus
- Diploneis crabro
- Diploneis ovalis
- Diploneis smithii
- diplostoma, Globigerina
- Dipsastraea, genus
- Dipsastraea speciosa
- Diptera, order
- Dipteridaceae, family
- Discoaster tamalis
- Discocyclina, genus
- discoidpoda, Trapa
- Discopulvinulina bradyi
- discorbinoides, Polystomellina
- Discorbis, genus
- discus subsp. hannai, Haliotis
- disjuncta, Conchocele
- dispar, Neptunea
- dissectum f. dissectum, Acer pictum
- dissectum, Acer pictum ssp. dissectum
- distans, Aulacoseira
- distans, Cladophlebis
- distans, Melosira
- distans var. osawae, Podozamites
- Distephanus speculum
- disticha, Metasequoia
- distichum, Taxodium
- distinctum, Flabellum
- Distoechodon, genus
- divaricata, Acila
- divaricata var. vigilia, Acila
- Divaricate nut clam
- divaricatum, Gafrarium
- divaricatus, Solecurtus
- diversifolia, Tsuga
- Dogfish shark
- Dog whelk, genus Nassarius
- Dog whelk, genus Nucella
- Dog winkle
- Dogwood
- dolabrata, Thujopsis
- doliaris, Ringicula
- Dolphin
- Domatoceras, genus
- Donacia katsurai
- Donaciinae, subfamily
- Donax cuneatus
- Donax semigranosus
- Door snail
- Dorcus (Nipponodorcus) rubrofemoratus
- Dorcus rubrofemoratus
- Dosinella angulosa
- Dosinella penicillata
- Dosinia, genus
- Dosinia akaisiana
- Dosinia angulosa
- Dosinia bilunulata
- Dosinia chikuzenensis
- Dosinia corrugata
- Dosinia ettyuensis
- Dosinia fujimotoi
- Dosinia hataii
- Dosinia japonica
- Dosinia japonica nomurai
- Dosinia kaneharai
- Dosinia (Kaneharaia) kaneharai
- Dosinia kannoi
- Dosinia kawagensis
- Dosinia nagaii
- Dosinia nomurai
- Dosinia ovata
- Dosinia penicillata
- Dosinia (Phacosoma) japonica
- Dosinia (Phacosoma) nomurai
- Dosinia shibaharensis
- Dosinia suketoensis
- Dosinia troscheli
- Dosinorbis, genus
- Dosinia (Phacosoma) troscheli
- Dosinorbis troscheli
- Double sculptured neptune
- Douglas fir
- douglasiae ssp. biwae, Nodularia
- douglasiae ssp. biwae, Unio
- Doxander, genus
- Doxander japonicus