- Acalolepta luxuriosa
- Acanthastrea hemprichii
- Acanthoceras, genus
- Acanthocircus bispinus
- acanthodon, Carcharhinus
- acanthodon, Negaprion
- Acanthogobius flavimanus
- Acanthohalysites kuraokaensis
- Acanthopagrus latus
- Acari, order
- Acer, genus
- Acer crataegifolium
- Acer diabolicum
- Acer ezoanum
- Acer honshuense
- Acer huziokae
- Acer japonicum
- Acer maximowiczianum
- Acer megasamarum
- Acer micranthum
- Acer miohenryi
- Acer miyabei
- Acer mono
- Acer mono var. glaucum
- Acer mono var. marmoratum
- Acer nikoense
- Acer nordenskioeldi
- aceroides, Platanus
- Acer palaeodiabolicum
- Acer palaeorufinerve
- Acer palmatum
- Acer palmatum var. amoenum
- Acer palmatum ssp. matsumurae
- Acer pictum ssp. dissectum f. dissectum
- Acer pictum ssp. glaucum
- Acer pictum ssp. mono
- Acer protomiyabei
- Acer pseudocarpinifolium
- Acer pseudoplatanus
- Acer rotundatum
- Acer rubrum var. ligniatum
- Acer rufinerve
- Acer saccharum
- Acer shirasawanum
- Acer sieboldianum
- Acer sieboldianum f. microphyllum
- Acer subpictum
- Acer tenuifolium
- Acer tottoriense
- Acer uweharae
- Acer yabei
- Acer yamanae
- Acer yoshiokaense
- Acesta, genus
- Acesta goliath
- Acesta yagenensis
- Acharax dalli
- Acharax johnsoni
- Acharax tokunagai
- Achnanthes inflata
- Achnanthes lanceolata
- Achnanthes oestrupii
- Achnanthidium lanceolatum f. lanceolatum
- aciculata, Neolitsea
- Acila, genus
- Acila (Acila) divaricata
- Acila (Acila) elongata
- Acila divaricata
- Acila divaricata var. vigilia
- Acila elongata
- Acila gottschei
- Acila hokkaidoensis
- Acila insignis
- Acila minuta
- Acila minutoides
- Acila mirabilis
- Acila musashiensis
- Acila nagaoi
- Acila nakazimai
- Acila oyamadaensis
- Acila oyamadensis
- Acila picturata
- Acila submirabilis
- Acilana, genus
- Acilana tokunagai
- Acilana tokunagai var. hayasakai
- Acila (Truncacila) gottschei
- Acila (Truncacila) hokkaidoensis
- Acila (Truncacila) insignis
- Acila (Truncacila) nakazimai
- Acila (Truncacila) picturata
- Acila vigilia
- Acipenseridae, family
- Acirsa martensi
- Acmaea pallida
- Acmaea sigaramiensis
- Acompsoceras renevierii
- Acosarina rectimarginata
- Acrilla densicostata
- Acropora, genus
- Acropora gemmifera
- Acrostichum, genus
- Acteocina exilis
- actilineata, Lucinoma
- Actinidia, genus
- Actinidia arguta
- Actinidia polygama
- Actinocyclus, genus
- Actinocyclus ehrenbergii
- Actinocyclus ingens
- Actinocyclus undulatus
- Actinocyathus japonicus
- Actinopterygii, class
- Actinoptychus splendens
- Actinoptychus undulatus
- Actinosphaera, genus
- aculeata, Bulimina
- acuminatum var. brebissonii, Gomphonema
- acuta, Fibularia
- acuta, Fibulariella
- acuta, Quercus
- acuticarinata, Cucullaea
- acutilineata, Lucina
- acutilineata, Lucinoma
- acutilineatum, Lucinoma
- acutipennis, Cladophlebis
- acutiplicatus, Enteletes
- Acutipula, subgenus
- acutissima, Quercus
- acutorostrata, Balaenoptera
- Adamnestia, genus
- adamsiana, Limopsis
- adamsii, Thylacodes
- adamsi, Protocallithaca
- Adams' thin shelled littleneck
- addita, Tegillarca
- Adelphic japelion
- adelphicus, Japelion
- Adiantites oaraiensis
- Adiantopteris ishidae
- adiastola, Plecia
- Adiozoptyxis hidakaensis
- Admete couthouyi
- Admete viridula
- admorsus, Nemotaulius
- adnata f. minores
- adstigmata, Betula
- Adulomya, genus
- Adulomya chitanii
- Adulomya uchimuraensis
- adunca, Pteropurpura
- adunca, Tritonalia
- aduncum, Ceratostoma
- aduncum, Ocinebra
- aduncus, Galeocerdo
- advenum, Elphidium
- akagii, Cyclocardia
- akagii, Venericardia
- akahirensis, Chlamys
- akaisiana, Dosinia
- akasakensis, Dentalium
- akasakensis, Neoschwagerina
- akasakensis, Waagenophyllum
- Akasakiella yabei
- akashiensis, Parastegodon
- akashiensis, Stegodon
- Akebiconcha chitanii
- Akebiconcha kawamurai
- akihoensis, Nipponopecten
- akihoensis, Placopecten
- akishimaensis, Eschrichtius
- Akishima whale
- akishimensis, Japonocetus
- akitaensis, Uvigerina
- akitana, Chlamys
- akitana, Ennucula
- akitanum, Umbonium
- akiyamae, Amussiopecten
- Akiyoshiella ozawai
- akiyoshiensis, Cyclemys
- akutsui, Chlamys
- alabaster, Nucella freycinetii
- Alangium, genus
- Alangium aequalifolium
- Alangium basiobliguum
- Alaska glass scallop
- Alaska jingle
- alaskense, Parvamussium
- alaskense, Polynemamussium
- alaskensis, Astarte
- alata, Pirenella
- alatus, Hinedorcus
- albardae, Sieboldius
- albicans naganumanus, Pecten
- albicans, Pecten
- Albicetus oxymycterus
- albida, Chlamys
- Albizia, genus
- Albizia miokalkora
- Albizzia miokalkora
- albocallosa, Amalda
- albocallosa, Amalda rubiginosa
- albocallosa okawai, Amalda
- albocallosa okawai, Baryspira
- albolineata, Glycymeris
- albolineata, Veletuceta
- Alces, genus
- Alchornea, genus
- alcokiana, Picea
- Alder
- Alder-leafed whitebeam
- aliena, Quercus
- Allodesmus, genus
- Allodesmus kernensis
- Almond yoldia
- alnifolia, Aria
- alnifolia, Sorbus
- Alnus, genus
- Alnus firma
- Alnus hirsuta
- Alnus hirsuta f. sibirica
- Alnus inokumae
- Alnus japonica
- Alnus maximowiczii
- Alnus miojaponica
- Alnus pendula
- Alnus protohirsuta
- Alnus protomaximowiczii
- Alnus serrulatoides
-
- Alnus subfirma
- Alnus tinctoria var. microphylla
- Alnus tsudae
- Alnus usyuensis
- alpina, Saxifraga fortunei
- Alpine black swallowtail
- Alpinoschwagerina minatoi
- alternifolia, Cardiandra
- alticostata, Lagena
- altisomus, Diplomystus
- altispira subsp. globosa, Globoquadrina
- altoumbonata, Glycymeris
- Alula, genus
- Alula elegantissima
- Alveinus, genus
- Alveinus ojianus
- Alveopora, genus
- Alveopora verrilliana
- amabile, Blechnum
- amabilis, Bolma
- amabilis, Galeoastraea
- amabilis, Paphia
- Amaea densicostata
- Amalda, genus
- Amalda albocallosa
- Amalda albocallosa okawai
- Amalda hilgendorfi
- Amalda hinomotoensis
- Amalda hinomotoensis subsp. urasima
- Amalda rubiginosa albocallosa
- Amalda urasima
- Amaltheus, genus
- Amauropsis sanchuensis
- ambigenus, Astriclypeus manni
- ambigenus, Astriclypeus mannii
- ambigua, Austiniceras
- ambigua, Parafusulina
- ambigua, Parapuzosia
- ambigua, Pseudofusulina
- ambigua, Rhus
- ambiguum, Ribes
- amblycephalus, Johnius
- Amblysiphonella, genus
- Ambrosia, genus
- amicitiae, Tambatitanis
- amicula, Anadara
- amicula elongata, Anadara
- amicula, Gifuella
- Amiiformes, order
- Ammonia beccarii
- Ammonia japonica
- Ammonia nipponica
- Ammonite
- Ammonoid
- Ammonoidea, subclass
- amoenum, Acer palmatum
- Amphibia, class
- Amphibian
- amphibia, Nitzschia
- amphiceros, Rhaphoneis
- Amphicoryna fukushimaensis
- Amphicoryna scalaris
- Amphidonte subhariotoidea
- amphipleuroides, Frustulia
- amphipleuroides, Frustulia rhomboides
- Amphipoda, order
- Amphipyndax tylotus
- Amphistegina lessonii
- Amphitragulus minoensis
- Amphora, genus
- Amphora ovalis
- Amphora ovalis var. pediculus
- Amphora pediculus
- Amplexocarinia radicula
- Amur barerry
- Amur cork tree
- amurense, Phellodendron
- amurensis, Berberis
- amurensis, Erodona
- amurensis var. japonica, Berberis
- amurensis, Maackia
- amurensis Phellodendron
- amurensis, Potamocorbula
- Amur maackia
- Amur maple
- Amur river clam
- Amusium, genus
- Amussiopecten akiyamae
- Amussiopecten iitomiensis
- Amussiopecten praesignis
- amussitata, Leptothyra
- amussitatum, Homalopoma
- amygdalea, Yoldia
- amygdalina, Salix
- Amygdalophyllum, genus
- Amynodon, genus
- anacanthus, Spondylus
- Anadara, genus
- Anadara abdita
- Anadara amicula
- Anadara amicula elongata
- Anadara (Anadara) amicula elongata
- Anadara (Anadara) makiyamai
- Anadara antiquata
- Anadara bisenensis
- Anadara broughtonii
- Anadara castellata
- Anadara chichibuensis
- Anadara daitokudoensis
- Anadara ferruginea
- Anadara granosa
- Anadara (Hataiarca) kakehataensis
- Anadara hataii
- Anadara hiratai
- Anadara kagoshimensis
- Anadara kakehataensis
- Anadara makiyamai
- Anadara ninohensis
- Anadara ogawai
- Anadara ommaensis
- Anadara satowi
- Anadara satowi castellata
- Anadara (Scapharca) abdita
- Anadara (Scapharca) broughtonii
- Anadara (Scapharca) hiratai
- Anadara (Scapharca) satowi
- Anadara (Scapharca) subcrenata
- Anadara subcrenata
- Anadara tatunokutiensis
- Anadara (Tegillarca) granosa
- Anadara (Tegillarca) granosa bisenensis
- Anadara watanabei
- Anagaudryceras, genus
- anakuma, Meles
- Ananchytes ovatus
- Anapachydiscus sutneri
- Anasibirites, genus
- Anastomopora, genus
- anatina, Lingula
- Anatolikos japonicus
- Anatotitan, genus
- Anchignathodus typicalis
- Anchitherium hypohippoides
- Anchovy
- Ancila okawai
- Ancistrolepis mogamiensis
- Ancistrolepis striatus
- Ancistrolepis togariensis
- Ancyloceras, genus
- andenensis, Haustator
- andenensis, Neohaustator
- andenensis, Turritella
- andersoni, Eothenomys
- andoi, Clinocardium
- andoi, Cryptonatica
- Andromeda, genus
- Angel shark
- Angiosperm
- Angiospermae, phylum
- anglica, Eoguttulina
- angulatosimile, Epitonium
- Angulogerina kokozuraensis
- angulosa, Dosinella
- angulosa, Dosinia
- angulosa, Nephrolepidina
- Angulus venulosa
- Angulus vestalioides
- angusta, Cylichnatys
- angustidens, Carcharodon
- angustidens, Lepus brachyurus
- angustidens, Otodus
- angustissima, Aulacoseira granulata
- angustissima, Melosira granulata
- angustum, Laevicardium
- angustum, Trachycardium
- aniensis, Cladrastis
- Anisocorbula ohiroi
- Anisocorbula venusta
- Anisomyon transformis
- Ankylosauria, infraorder
- Annamocarya sinensis
- annectens, Gomphotherium
- Annelid
- Annelida, phylum
- annulata, Lucinoma
- annulata, Schuettia
- annulata, Spinotriassocampe
- annulata, Yeharaia
- annulatum, Triceratium
- Annuliconcha, genus
- Anodonta, genus
- Anodonta calipygos
- Anodonta matajiroi
- Anodonta okuyamai
- Anodonta woodiana
- Anodontia, genus
- Anodontia stearnsiana
- Anodontophora, genus
- Anomalina
- Anomalocardia squamosus
- Anomalodiscus, genus
- Anomalodiscus squamosus
- Anomia, genus
- Anomia chinensis
- Anomia cytaeum
- Anomia ephippium
- Anomia lischkei
- Anoplophora malasiaca
- Anotopterus, genus
- Anourosorex japonicus
- Ant
- Antalis weinkauffi
- Anthoathecata, order
- Anthocidaris, genus
- Anthonya japonica
- Anthonya subcantiana
- Anthozoa, class
- Antillophos fusiforme
- Antiplanes contraria
- antipofi, Fagus
- Antiplanes sanctiioannis
- Antiplanes vinosa
- antiqua, Carcinoplax
- antiquata, Anadara
- antiqua, Thalassiosira
- Antique ark
- Anura, order
- Arachnoidiscus ehrenbergii
- araii, Cuspidaria
- arakawai, Chlamys
- arakawensis, Modiolus
- Aralia, genus
- Aralia cordata
- aralioides, Trochodendron
- aralioides var. longifolium, Trochodendron
- Araneae, order
- Araneidae, family
- Araucarioxylon, genus
- Arca, genus
- Arca boucardi
- Arca boucardi miyatensis
- Arca miyatensis
- Arca ocellata
- Arca watanabei
- Archaeodictyomitra, genus
- Archaeognatha, order
- Archaeohagiastrum munitum
- Archaeolithothamnium, genus
- Archaeosemantis cristianensis
- Archaeosemantis venusta
- Archaeospongoprunum, genus
- Archaeospongoprunum imlayi
- Archaeospongoprunum tenue
- Archaeozostera, genus
- Archaeozostera longifolia
- Architectonica yokoyamai
- architemporaria, Rana
- Arcidae, family
- arctata, Macoma
- Arctic moonsnail
- Arctic surfclam
- arcticum, Equisetites
- arcticum, Equisetum
- Arcopsis interplicata
- Arctoprionites, genus
- Arctostrea, genus
- Arctostrea carinata
- arctos, Ursus
- Arcuatula, genus
- Ardeidae, family
- Arecaceae, family
- arenaria, Mya
- arenaria oonogai, Mya
- Arenomya grewingki
- Arenomya grewingki var. elongata
- argenteonitens, Bathybembix
- argenteonitens convexiusculus, Bathybembix
- argenteonitens, Ginebis
- argenteonitens hirasei, Ginebis
- argenteostriatus, Pleioblastus
- argenteus, Apodemus
- Arges parallelus
- Argonauta awaensis
- Argonauta itoigawai
- Argonautidae, family
- arguta, Actinidia
- Aria, genus
- Aria alnifolia
- Aria japonica
- Arieticeras, genus
- Ariosoma meeki
- Ark clam
- armata, Stylocoeniella
- Artemisia genus
- Artemisia indica var. maximowiczii
- Artemisia princeps
- arthritica, Neptunea
- arugai, Meretrix
- Aruncus dioicus var. kamtschaticus
- asagaiensis, Clinocardium
- asagaiensis, Macoma
- asagaiensis, Neverita
- asagaiensis, Yoldia
- asahiensis, Thracia
- Asamiella japonica
- asanoi, Chicoreus
- asanoi, Euomphalus
- asanoi, Rhizophorimurex
- asanoi, Straparollus
- Ascopora, genus
- Ash
- ashiyaensis, Chlamys
- ashiyaensis, Euspira
- ashiyaensis, Fulgoraria
- ashiyaensis, Pitar
- Asian beaked hazel
- Asian black bear
- Asian common ladyfern
- Asian hazel
- Asian hornbeam
- Asian paddle crab
- Asian rapa whelk
- asianus, Chicoreus
- Asian wild ass
- asiatica, Phricodothyris
- asiatica, Squamularia
- Asilidae, family
- Aspalima crenata
- aspera, Echinophyllia
- aspera kioroshiensis, Venerupis
- aspera, Venerupis
- asperella, Merica
- asper, Favosites
- aspersa, Glycymeris
- aspersa, Siphonalia
- asperulata, Chlamys
- asperulata, Mimachlamys
- Astarte, genus
- Astarte alaskensis
- Astarte borealis
- Astarte crenata
- Astarte filatovae
- Astarte hakodatensis
- Astartella, genus
- Astarte multicostata
- Astarte striata
- Astarte subsenecta
- Astarte (Tridonta) borealis
- Asteraceae, family
- Asteria, genus
- Asterozoa, subphylum
- Astraea, genus
- Astraea furuichii
- Astraea hayakawai
- Astraea omorii
- astraea, Stephanodiscus
- Astralium, genus
- astrata, Corbicula
- astrata, Corbicula fuscata
- Astrea, genus
- Astrea curta
- Astriclypeus, genus
- Astriclypeus integer
- Astriclypeus manni ambigenus
- Astriclypeus mannii
- Astriclypeus mannii ambigenus
- Astriclypeus mannii minoensis
- Astriclypeus minoensis
- Astrocentrus, genus
- Astrononion aomoriense
- Astropecten, genus
- asuwensis, Nilssonia
- aswaensis, Tedorosaurus
- asymmetrosa, Pterocarya
- Atactodea, genus
- Atactodea striata
- atava, Neithea
- atavus, Neithea
- Ataxioceras, genus
- Atetsuella, genus
- Athleta, genus
- Athleta japonica
- Athleta nishimurai
- Athleta (Volutospina), genus
- Athyrium yokoscense
- Atrina, genus
- Atrina japonica
- Atrina pectinata
- attenuatus, Cultellus
- attramentaria, Batillaria
- Aturia, genus
- Aturia coxi
- Aturia minoensis