- Babylonia, genus
- Babylonia elata
- Babylonia japonica
- Babylonia kozaiensis
- Babylonia lutosa
- bacchus, Nipponites
- Bacillariophyceae, class
- bacillum, Navicula
- bacula, Potamides
- bacula, Vicaryella
- Baculites, genus
- Baculites inornatus
- baculoide, Sciponoceras
- baculoides, Favosites
- Badger
- Baetis, genus
- bagualensis, Camerina
- baguelensis, Nummulites
- Baiera, genus
- Baiera lindleyana
- Bakevellia, genus
- Bakevellia haradae
- Bakevellia nagatoensis
- Bakevellia (Neobakevellia) shinanoensis
- Bakevellia (Neobakevellia) trigona
- Bakevellia shinanoensis
- Bakevellia trigona
- Bakevelloides (Yoshimopsis) nagatoensis
- bakko, Salix
- Balaenoptera, genus
- Balaenoptera acutorostrata
- Balaenoptera borealis
- Balaenopteridae, family
- Balaenura, genus
- Balanomorpha, subclass
- Balanophyllia (Eupsammia) imperialis
- Balanophyllia imperialis
- balantium, Clio
- balantium, Euclio
- Balanus, genus
- Balanus tintinnabulum rosa
- Bald cypress
- Baleen whale
- balsamoides, Populus
- balticus, Cataoceramus
- balticus, Inoceramus
- Bamboo
- Bamboo-leaf oak
- Bambusoideae, subfamily
- bambusoides, Phyllites
- bambusoides, Phyllostachys
- barbarense, Elphidium fax
- Barbatia, genus
- Barbatia bistrigata
- Barbatia foliata
- Barbatia kubara
- Barbatia lima
- Barbatia minoensis
- Barbatia stearnsii
- Barbatia virescens
- Barberry
- barbinervis, Clethra
- barleeanus, Melonis
- Barnacle
- Barnea, genus
- Barnea (Anchomasa) manilensis inornata
- Barnea dilatata
- Barnea japonica
- Barnea manilensis
- Barnea manilensis inornata
- Barnea (Umitakea) japonica
- Barrel-bubble snail
- Baryspira albocallosa okawai
- Basidiomycota, phylum
- Basilissa (Orectospira) nenokamiensis
- basiobliguum, Alangium
- Basket cockle
- Basterotia gouldi
- Bathrotomaria, genus
- Bathrotomaria yokoyamai
- Bathybembix argenteonitens
- Bathybembix argenteonitens convexiusculus
- Bathygobius, genus
- Bathynomus, genus
- bathyrhaphe, Granuliterebra
- Bathytoma luehdorfi
- Bathytormus foveolatus
- Batillaria, genus
- Batillaria attramentaria
- Batillaria cumingii
- Batillaria mizunamiensis
- Batillaria multiformis
- Batillaria toshioi
- Batillaria zonalis
- Batillus, genus
- Batoid
- Batoidea, superorder
- Batostomella, genus
- Beaked hickory
- Bear
- Bearded croaker
- beccarii, Ammonia
- beccarii, Rotalia
- Bedeva, genus
- Beech
- Beedeina, genus
- Beedeina fujimotoi
- Beedeina lanceolata
- Beetle
- Behemotops, genus
- Belemnite
- Belemnoid
- Belemnoidea, order
- Bellamya kosasana
- Bellamya suzukii
- Bellerophon, genus
- Bellerophon jonesianus
- Belleza decora
- bellula, Plicarcularia
- bellulus, Nassarius
- bengalensis subsp. chinensis, Prionailurus
- Bennettitales, order
- Benthamidia, subgenus
- Benthamidia japonica
- Bent-winged bat
- Benzoin membranaceum
- Berberis, genus
- Berberis amurensis
- Berberis amurensis var. japonica
- berchemiaefolia, Berchemiella
- Berchemia miofloribunda
- Berchemia racemosa
- Berchemiella berchemiaefolia
- Berchemiella berchemiifolia
- berchemiifolia, Berchemiella
- Bering sea cockle
- bernardi, Oxyperas
- Bernard's venus
- Berriasella, genus
- besshoense, Aelga
- besshoense, Periploma
- bessonowi, Helicoprion
- Betula, genus
- Betulaceae, family
- Betula adstigmata
- Betula costata
- Betula dahurica
- Betula davurica
- Betula ermanii
- Betula grossa
- Betula hommashinichii
- Betula maximowicziana
- Betula miomaximowicziana
- Betula nathorsti
- Betula nikoensis
- Betula nipponica
- Betula onbaraensis
- Betula platyphylla
- Betula protoermanii
- Betula protoglobispica
- Betula sadoensis
- Betula schmidtii
- Betula sekiensis
- Betula uzenensis
- Bevahites, genus
- bialata, Pegophysema
- Bibio, genus
- Bibionidae, family
- Bibio sadoensis
- bicarinata, Trichotropis
- bicincta, Mitrella
- bicolor, Picea
- biconcavus, Spongodiscus
- biconica, Fusulinella
- biconica, Siphonalia declivis
- Biddulphia tridentata f. tridentata
- Biddulphia tuomeyi var. tridentata
- bifrons, Rectobolivina
- bifrons ugariensis, Pristiterebra
- bihamatus, Lyristes
- biloba, Latiproetus
- biloba, Prantlia
- bilunulata, Dosinia
- biplicata, Cylichna
- Birch
- Bird
- biremis, Yoldia
- bisecta, Conchocele
- bisecta var. nipponica, Thyasira
- bisecta, Thyasira
- bisenensis, Anadara
- bisenensis, Anadara (Tegillarca) granosa
- Bison, genus
- Bison hanaizumiensis
- bispinosa var. makinoi, Trapa
- bispinus, Acanthocircus
- bispinus, Spongosaturnalis
- bistrigata, Barbatia
- bistrigata, Mesocibota
- bistrigata, Nipponarca
- biternata, Clematis apiifolia
- Bittersweet clam
- Bittium, genus
- Bittium horinjiense
- Bittium s-satoi
- Bittium (Stylidium) horinjiense
- Bivalve
- Bivalvia, class
- biwae, Nodularia douglasiae
- biwae, Unio douglasiae
- Biwamelania gamoensis
- Biwamelania multigranosa
- bocki, Fusulinella
- boeddinghausi, Hiatula
- Boehmeria tricuspis
- Bogbean
- Bohdi tree
- bohemicus, Heliolites
- Bolivina robusta
- Bolivina seminuda
- Bolivinita quadrilatera
- Bolma amabilis
- Bolma guttata
- bombycis, Morus
- Bonnet shell
- borealis, Astarte
- borealis, Balaenoptera
- borealis, Globigerina
- borealis, Hemitrapa
- borealis, Pinnularia
- Boreoscala yokozunai
- Boreotrophon, genus
- Boreotrophon candelabrum
- Boreotrophon kagana
- Boreotrophon xestra
- Borniopsis, genus
- Borniopsis tsurumaru
- Bositra, genus
- Boston ivy
- boucardi, Arca
- boucardi miyatensis, Arca
- Bovini, tribe
- Bowdenatheca, genus
- Brachidontes modiolus
- Brachopod
- Brachopoda, phylum
- brachybotrys, Wisteria
- Brachyphyllum, genus
- Brachyphyllum japonicum
- Brachystomia, genus
- Brachyura, infraorder
- brachyurus subsp. angustidens, Lepus
- Braconidae, family
- Braconid wasp
- bracteosus, Equisetites
- bracteosus, Equisetostachys
- bradyi, Discopulvinulina
- Bradyina, genus
- bradyi, Rosalina
- Brasenia purpurea
- Brasenia schreberi
- braunsi, Clinocardium
- braunsi, Dinocardium
- braunsi, Drillia
- braunsi, Eocylichna
- braunsi, Fuscocardium
- braunsi, Pleurotoma
- brebissonii var. diminuta, Pinnularia
- brebissonii, Gomphonema acuminatum
- Brechites yokoyamai
- bredanensis, Steno
- Brevimyurella japonica
- breviora, Haeckelicyrtium
- brevipinna, Carcharhinus
- brevis, Echinarchnius
- brevisiphonata, Ezocallista
- brevis, Scaphechinus
- brevistriata, Fragilaria
- brevitesta, Bucardiomya
- brevitesta, Pholadomya
- Bridalwreath spiraea
- Brisingella, genus
- Brisingidae, family
- Brissopsis, genus
- Brissopsis makiyamai
- Brittle star
- Broad-tooth wihite shark
- bronni, Reishia
- bronni, Thais
- Brotiopsis wakinoensis
- broughtonii, Anadara
- broughtonii, Anadara (Scapharca)
- Brown algae
- Brown bear
- brueggemanni, Turbinaria
- Bruguiera, genus
- Bryophyta, phylum
- Bryozoa, phylum
- Bryozoan
- Bucardiomya brevitesta
- Buccella tanaii
- Buccinidae, family
- buccinulum, Dentalium
- Buccinum, genus
- Buccinum glaciale
- Buccinum leucostoma
- Buccinum middendorfii
- Buccinum mogamiensis
- Buccinum ochotense
- Buccinum Schantaricum
- Buccinum Sinanoense
- buchiana, Cycadeoidea
- buchianum, Zamiophyllum
- buchianus, Zamites
- Buckbean
- Bufo, genus
- Bufo japonicus
- bulgarica, Neogondolella
- Bulimina, genus
- Bulimina aculeata
- Bulimina marginata
- bulloides, Globigerina
- burchardi, Mitrella
- burejensis, Coniopteris
- Burned nassa
- Burnet
- Bur-reed
- Burseolina pacifica
- busoensis, Cryptomya
- Butterfly ray
- Butternut
- buxifolium, Syzygium
- Buxus microphylla
- Buxus microphylla var. japonica