- Rabbit
- Raccoon dog
- racemosa, Berchemia
- raciborskii, Cladophlebis
- radiata, Terebratalia
- radiatostriata, Costocyrena
- radiatostriata, Cyrena
- radiatostriata, Polymesoda
- radicula, Amplexocarinia
- radicula, Nodosaria
- Radiolaria
- Radiolarian
- radiola, Volvulella
- radiolus, Rhizorus
- radiosa, Navicula
- Radiozoa, phylum
- Raeta, genus
- Raeta pellicula
- Raeta pulchella
- Raeta (Raetina) pellicula
- Raeta yokoyamaensis
- Raetellops pulchellus
- Raetina pulchella
- Raetina pellicula
- Ragworm
- Raha, genus
- Raha yabei
- ramosus, Nipponophycus
- Rana architemporaria
- Rana shiobarensis
- randolphi, Pecten
- Rapana rapiformis
- Rapana thomasiana
- Rapana venosa
- Raphinesquina, genus
- Raphitomidae, family
- rapiformis, Rapana
- raris, Kubikichthys
- raritatis, Cavolinia
- Rastellum, genus
- Rastellum (Arctostrea) carinatum
- Rastellum carinatum
- Rastellum diluvianum
- Ray
- Ray-finned fish
- Razor clam
- rectangularis, Neoconularia
- rectangulus, Cultellus
- rectimarginata, Acosarina
- Rectiplanes sanctiioannis
- Rectobolivina bifrons
- recurva, Clio
- Red algae
- Red-bark oak
- Redfin dace
- Red-throated loon
- Redvein enkianthus
- Reed grass
- Reedops nonakai
- refulgens, Cibicides
- regale, Nannobrachium
- regularis, Inoceramus
- Reichelina, genus
- reiniana, Glossaulax
- reiniana, Neverita
- reinianus, Inversiunio
- reinii, Nageia
- reinii, Podozamites
- Reishia, genus
- Reishia bronni
- Reishia clavigera
- renevierii, Acompsoceras
- reniformis, Dictyozamites
- Repomucenus lunatus
- Reptile
- Reptilia, class
- reticulata, Clathrofenella
- Reticunassa, genus
- Reticunassa festiva
- Reticunassa japonica
- Reticunassa simizui
- retiformis, Fenestella
- Retifusus virens
- Retifusus virens tenuis
- Retiophyllia, genus
- Retiophyllia wasabidaniensis
- retroversa, Pseudochama
- Retusidae, family
- Reussella, genus
- Reussoolina laevis
- Rexithaerus sectior
- Reynoutria japonica
- Reynoutria sachalinensis
- Rhabdonema, genus
- rhabdotum, Dentalium
- rhabdotum, Striodentalium
- Rhamnus, genus
- Rhaphoneis amphiceros
- Rhinoceros
- Rhinocerotidae, family
- Rhinoclavis, genus
- Rhinoclavis kochi
- Rhinoclavis tokiensis
- Rhinogobius, genus
- Rhinolophidae, family
- Rhinolophus cornutus
- Rhinophoridae, family
- Rhizophorimurex asanoi
- Rhizophorimurex tiganouranus
- Rhizorus radiolus
- Rhizosolenia hebetata
- Rhizosolenia semispina
- Rhizosphaera, genus
- Rhododendron, genus
- Rhododendron degronianum
- Rhododendron dilatatum
- Rhododendron kaempferi
- Rhododendron metternichii var. pentamerum
- Rhododendron quinquefolium
- Rhododendron tatewakii
- Rhododendron wadanum
- Rhodopetoma erosa
- Rhodophyllum, genus
- Rhodophyta, phylum
- Rhoicosphenia abbreviata
- Rhoicosphenia curvata
- rhoifolia, Pterocarya
- rhombica, Saccella
- rhombica, Yoldia
- rhombicum, Leptophloeum
- rhomboides var. amphipleuroides, Frustulia
- Rhopalodia gibberula
- Rhopalodia rupestris
- Rhus ambigua
- Rhus miosuccedanea
- Rhus protoambigua
- rhynchophylla, Fraxinus chinensis
- rhynchophysa, Carex
- Ribes ambiguum
- Ribes fasciculatum
- Richthofenia, genus
- richthofeni, Chione
- richthofeni, Chione (Gnidiella)
- richthofeni, Chionopsis
- richthofeni, Leptodus
- Righteye flounder
- rigida, Juniperus
- rigida, Nerinea
- rikuchuensis, Globorotalia
- Ringicula, genus
- Ringicula doliaris
- Ringicula shimaensis
- Ringicula yokoyamai
- Ringiculina, genus
- Ringiculopsis itoigawai
- River snail
- Rivularia, genus
- Robaia robai
- robai, Nuculana
- robai, Robaia
- Robber fly
- robillardi, Epitonium
- Robulus, genus
- Robulus nikobarensis
- robusta, Bolivina
- robusta, Hiscocapsa
- robusta, Lobophyllia
- robustus, Coscinodiscus robustus
- robustus, Endictya
- robustus f. robustus, Coscinodiscus
- robustus, Wakinoichthys
- Rodentia, order
- Rodgersia podophylla
- Romaleon gibbosulum
- rorida, Salix
- Rorqual whale
- Rosa, genus
- rosa, Balanus tintinnabulum
- rosacea, Dendostrea
- Rosaceae, family
- Rosalina bradyi
- Rosalina globularis
- rosa, Megabalanus
- Rosa multiflora
- Rosa usyuensis
- Rose
- Rose-branch murex
- roseomaculatus, Solen
- Rosselia, ichnogenus
- rostrata, Navicula placentula
- rostrata, Placoneis placentula
- Rotalia, genus
- Rotalia beccarii
- Rotalia nipponica
- rotulata, Lenticulina
- rotunda, Glycymeris
- rotunda, Neoschwagerina
- rotundatum, Acer
- Rough-toothed dolphin
- Rove beetle
- rubellus, Laqueus
- ruber, Globigerinoides
- rubiginosa albocallosa, Amalda
- rubrofemoratus, Dorcus
- rubrofemoratus, Nipponodorcus
- rubroidea, Quercus
- rubrum, Flabellum
- rubrum var. ligniatum, Acer
- rubrum, Monomyces
- Rubus crataegifolius
- Rubus palmatus
- Rubus palmatus f. palmatus
- Rudist
- Ruditapes, genus
- Ruditapes miyamurensis
- Ruditapes philippinarum
- Ruditapes variegata kioroshiensis
- Ruditapes variegatus
- rufinerve, Acer
- rufocanus, Clethrionomys
- rufocanus, Craseomys
- rugicollis, Apriona
- Rugosa, order
- rugosa, Styrax
- Rugososchwagerina yabei
- rugosus, Styrax
- rupestris, Rhopalodia
- russa, Cryptonatica
- rusticus, Omphalius