- Yaadia japonica
- Yaadia kimurai
- yabei, Acer
- yabei, Akasakiella
- yabei, Cassidulina
- Yabeiceras, genus
- yabei, Crassatella
- yabei, Crassatellites
- yabei, Ctenis
- Yabeiella, genus
- yabei, Epitonium
- yabei, Eucrassatella
- yabei, Japelion
- yabei, Kueichouphyllum
- yabei, Liquidambar
- yabei, Maedagonia
- yabei, Mauremys
- yabei, Mitrella
- yabei, Mizzia
- yabei, Murchisonia
- Yabeina, genus
- Yabeina globosa
- Yabeina inouyei
- Yabeina kaizensis
- Yabeina multiseptata
- Yabeina shiraiwensis
- yabei, Palaeoloxodon namadicus
- yabei, Parafusulina
- yabei, Pyrgo
- yabei, Raha
- yabei, Rugososchwagerina
- yabei, Schwagerina
- yabei, Sinomegaceroides
- yabei, Sinomegaceros
- yabei, Spiromphalus
- yabei, Thalassiosira
- yabei, Uvigerina
- Yabepecten ogasawarai
- Yabepecten tokunagai
- yabunikkei, Cinnamomum
- yagenensis, Acesta
- yagenensis, Lima
- yagurai, Chlamys
- yagurai, Volachlamys
- yamadensis, Tectus
- yamagatana, Yoldia
- yamakawai, Pillucina
- yamakoshii, Gravicalymene
- yamanae, Acer
- yamanarii, Tateiwaia
- yamanei, Geloina
- yamasakii, Glycymeris
- yamasakii kintaichiensis, Patinopecten
- yamasakii, Kotorapecten
- yamasakii, Mizuhopecten
- yamasakii, Patinopecten
- yamasugensis, Tropidelasma
- yamazakii, Guttulina
- yanagawaensis, Aequipecten
- yanagawaensis, Cryptopecten
- yanagidai, Chuhsiungichthys
- yanagidaniensis, Fulgoraria
- yanagidaniensis, Musashia
- yanagidaniensis, Psephaea
- yanagisawai, Endops
- yanamii, Mohnia
- yanamii tenuis, Mohnia
- Yangchienia, genus
- yasudae, Parvamussium
- yasudae, Polynemamussium
- yato, Lycocerus
- Yatsengia, genus
- yatsuoensis, Cerithidea
- yatsuoensis, Cerithideopsilla
- yatsuoensis, Nucella
- yatsuoensis, Pirenella
- yatsuoensis, Polytropa
- Yeharaia annulata
- Yeharaia cornigera
- Yeharaia japonica
- Yeharalla ainuana
- Yellowfin goby
- Yellowfin bream
- Yellowhorn
- Yellow-mouth buccinum
- Yellow mussel
- Yellowwood
- yendoi, Iravadia
- yendoi, Pseudonoba
- yendoi, Sinusicola
- yesoensis, Cervus nippon
- yessoensis, Glycymeris
- yessoensis, Mizuhopecten
- yessoensis, Patinopecten
- yessoensis yokoyamae, Mizuhopecten
- yessoensis yokoyamai, Patinopecten
- Yesso scallop
- Yew
- yezoense, Ailanthus
- yezoensis, Mertensia pterocarpa
- Yezosaurus
- yokoyamaensis, Raeta
- yokoscense, Athyrium
- yokoyamae, Hemitrapa
- Yokoyamaella tertioseptata
- yokoyamae, Mizuhopecten
- yokoyamae, Mizuhopecten yessoensis
- yokoyamai, Architectonica
- yokoyamai, Bathrotomaria
- yokoyamai, Brechites
- yokoyamai, Corbula
- yokoyamai, Crenella
- yokoyamai, Diodora
- yokoyamai, Fissidentalium
- yokoyamai, Foegia
- yokoyamai forma japonica, Potamides
- yokoyamai forma japonica, Vicarya
- yokoyamai koshibensis, Diodora
- yokoyamai kosibensis, Diodora
- yokoyamai, Mercenaria
- yokoyamai, Nanonavis
- yokoyamai, Nassaria magnifica
- yokoyamai, Neptunea
- yokoyamai, Nipponoclava
- yokoyamai, Nipponomaria
- yokoyamai, Nuculana
- yokoyamai, Nuculana (Thestyleda)
- yokoyamai, Onychiopsis
- yokoyamai, Patinopecten yessoensis
- yokoyamai, Periploma
- yokoyamai, Pleurotomaria
- yokoyamai, Potamides
- yokoyamai, Propebela
- yokoyamai, Pseudoperissolax
- yokoyamai, Ringicula
- yokoyamai, Serripes
- yokoyamai, Spisula
- yokoyamai, Tetoria
- yokoyamai, Thestyleda
- yokoyamai, Varicorbula
- yokoyamai, Vicarya
- yokoyamai, Vicarya verneuili
- yokozunai, Boreoscala
- yokozunai, Epitonium
- Yoldia, genus
- Yoldia amygdalea
- Yoldia asagaiensis
- Yoldia biremis
- Yoldia (Cnesterium) johanii
- Yoldia (Cnesterium) notabilis
- Yoldia (Cnesterium) yamagatana
- Yoldia johanii
- Yoldia laudabilis
- Yoldia lischkei
- Yoldia naganumana
- Yoldia notabilis
- Yoldia rhombica
- Yoldia sagittaria
- Yoldia similis
- Yoldia thraciaeformis
- Yoldia tokunagai
- Yoldia yamagatana
- Yoldia (Yoldia) biremis
- yonegafukuroensis, Leucosyrinx
- yoshidae, Ecdyonurus
- yoshidai, Turritella
- yoshidai, Venericardia
- yoshidense, Laevicardium
- yoshidensis, Conus
- yoshiokaense, Acer
- yoshiokaensis, Torreya
- yoshiwarai, Echinolampas
- yoshiwarai, Mikadotrochus
- yoshiwarai, Perotrochus
- yoshiwarai, Pleurotomaria
- youngi, Panthera
- yowarensis, Millerella
- yowarensis, Neomillerella