- obassia, Styrax
- obassis, Styrax
- Obesotoma, genus
- obliquata, Pseudogramatodon dalli
- obliquecostata, Apiotrigonia
- obliquiloculata, Pulleniatina
- obliquus, Carcharias
- obliquus, Otodus
- oblonga, Crenulilimopsis
- oblongata, Crassatellites
- oblongata, Indocrassatella
- oblongifolia, Trizygia
- oborensis, Lithophyllum
- obounta, Cephalotaxus
- obovata, Magnolia
- obscuriformis, Pinnularia
- obsoletiformis, Parallelodon
- obtusata, Hamamelis japonica
- obtusicauda, Pseudophillipsia
- obtusiloba, Lindera
- Ocadia, genus
- Ocadia sinensis
- Ocadia tanegashimensis
- occidentalis, Metasequoia
- Oceanic dolphin
- ocellata, Arca
- ocellata, Cyclotella
- Ocenebra inornata
- Ochetoclava kochi
- ochiaiensis, Cyclocardia
- ochotense, Buccinum
- ochotica var. densistriata, Entomonotis
- ochotica var. densistriata, Monotis
- ochotica, Entomonotis
- ochotica var. eurachis, Entomonotis
- ochotica var. eurachis, Monotis
- ochotica, Monotis
- Ocinebra aduncum
- Ocinebrellus, genus
- Ocinebrellus falcatus
- Octangonal tusk shell
- octangulatum, Dentalium
- octangulatum hexagonum, Dentalium
- octotuberculata, Trapa
- oculata, Madrepora
- Opalia matajiroi
- opercularis, Glabratella
- opercularis, Planoglabratella
- Operculina, genus
- Operculina complanata
- Operculina complanata var. japonica
- Operculina japonica
- Ophiacantha, genus
- Ophiceras, genus
- Ophiodermella miyatensis
- Ophiodermella ogurana
- Ophiodermella pseudopannus
- Ophiomorpha, ichnogenus
- Ophiothrix, genus
- Ophiuroidea, class
- Opis torinosuensis
- optapa, Odostomia
- optiva, Macoma
- orbicularis, Cyclammina
- orbicularis, Gyroidina
- orbiculata, Macoma
- orbiculata, Nilssonia
- orbiculatus, Celastrus
- Orbiculiforma, genus
- orbignyana, Fissurina
- Orbitolina, genus
- Orbitolina lenticularis
- Orbulina, genus
- Orbulina universa
- Orb-weaver spider
- Orectospira, genus
- Orectospira nenokamiensis
- oregonensis, Fusitriton
- oregonensis, Priene
- oregonensis, Triton
- Oregon hairy triton
- Oriensarctos watasei
- Oriental bittersweet
- orientale, Hyphantoceras
- orientale, Toxicodendron
- Oriental flower beetle
- orientalis, Cyclina
- orientalis, Deltocyathoides
- orientalis, Dineutus
- orientalis, Inoceramus
- orientalis, Myophorella
- orientalis, Nelumbo
- orientalis, Nilssonia
- orientalis, Nisaetus nipalensis
- orientalis, Notocyathus
- orientalis, Paradeltocyathus
- orientalis, Protaetia
- orientalis, Spizaetus nipalensis
- orientalis, Stegodon
- Oriental white oak
- Ornithomimid
- Ornithomimidae, family
- Ornithopod
- Ornithopoda, suborder
- Orthaulax japonicus
- Orthoceras, genus
- Orthoceratoid
- Orthocerida, order
- Orthotichia japonica
- osawae, Cycadocarpidium
- osawae, Podozamites distans
- osawanoensis, Limopsis
- osawanoensis, Noditerebra
- osawanoensis, Oxyperas
- osawanoensis, Terebra
- Osmanthus chaneyi
- Osmanthus heterophyllus
- Osmunda, genus
- osozawaensis, Glycymeirs
- Osteoglossiformes, order
- Ostericum sieboldii
- Ostracod
- Ostracoda, class
- Ostrea, genus
- Ostrea circumpicta
- Ostrea (Crassostrea) gravitesta
- Ostrea denselamellosa
- Ostrea gigas
- Ostrea gravitesta
- Ostreoidea, superfamily
- Ostrya, genus
- Ostrya shiragiana
- otai, Aokiichthys
- otaniensis, Calliostoma
- Otariidae, family
- Otodus angustidens
- Otodus obliquus
- otoensis, Perotrochus
- otohimeae, Pendaloma
- Otostoma japonicum
- Otozamites, genus
- Otozamites fujimotoi
- Otozamites kondoi
- otsukai, Costocyrena
- otukae, Chlamys
- otukai, Cultellus
- otukai, Lucinoma
- otutumiensis, Nanaochlamys notoensis
- ovalifolia var. elliptica, Lyonia
- ovalis, Amphora
- ovalis, Diploneis
- ovalis, Heteropsammia
- ovalis var. japonica, Heteropsammia
- ovalis var. pediculus, Amphora
- ovalis, Pinnularia
- ovata, Dosinia
- ovata, Euspira pila
- ovata, Lunatia pila
- ovata, Portlandia
- ovatocarpa, Carya
- ovatus, Ananchytes
- ovatus, Echinocorys
- Oviraptorid
- Oviraptoridae, family