- 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門
- Raeta属
- Raeta pellicula
- Raeta pulchella
- Raeta (Raetina) pellicula
- Raeta yokoyamaensis
- Raetellops pulchellus
- Raetina pellicula
- Ragworm
- Raha属
- Raha yabei
- ramosus, Nipponophycus
- Rana architemporaria
- Rana shiobarensis
- randolphi, Pecten
- Rapana rapiformis
- Rapana thomasiana
- Rapana venosa
- Raphinesquina属
- Raphitomidae科
- rapiformis, Rapana
- raris, Kubikichthys
- raritatis, Cavolinia
- Rastellum属
- 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属
- reiniana, Glossaulax
- reiniana, Neverita
- reinianus, Inversiunio
- reinii, Nageia
- reinii, Podozamites
- Reishia属
- Reishia bronni
- Reishia clavigera
- renevierii, Acompsoceras
- reniformis, Dictyozamites
- Repomucenus lunatus
- Reptile
- Reptilia網
- reticulata, Clathrofenella
- Reticunassa属
- Reticunassa festiva
- Reticunassa japonica
- Reticunassa simizui
- retiformis, Fenestella
- Retifusus virens
- Retifusus virens tenuis
- Retiophyllia属
- Retiophyllia wasabidaniensis
- retroversa, Pseudochama
- Retusidae科
- Reussella属
- Reussoolina laevis
- Rexithaerus sectior
- Reynoutria japonica
- Reynoutria sachalinensis
- Robaia robai
- robai, Nuculana
- robai, Robaia
- Robber fly
- robillardi, Epitonium
- Robulus属
- Robulus nikobarensis
- robusta, Bolivina
- robusta, Hiscocapsa
- robusta, Lobophyllia
- robustus, Coscinodiscus robustus
- robustus, Endictya
- robustus f. robustus, Coscinodiscus
- robustus, Wakinoichthys
- Rodentia目
- Rodgersia podophylla
- Romaleon gibbosulum
- rorida, Salix
- Rorqual whale
- Rosa属
- rosa, Balanus tintinnabulum
- rosacea, Dendostrea
- Rosaceae科
- Rosalina bradyi
- Rosalina globularis
- rosa, Megabalanus
- Rosa multiflora
- Rosa usyuensis
- Rose
- Rose-branch murex
- roseomaculatus, Solen
- Rosselia属
- rostrata, Navicula placentula
- rostrata, Placoneis placentula
- Rotalia属
- 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属
- Ruditapes miyamurensis
- Ruditapes philippinarum
- Ruditapes variegata kioroshiensis
- Ruditapes variegatus
- rufinerve, Acer
- rufocanus, Clethrionomys
- rufocanus, Craseomys
- rugicollis, Apriona
- Rugosa目
- rugosa, Styrax
- Rugososchwagerina yabei
- rugosus, Styrax
- rupestris, Rhopalodia
- russa, Cryptonatica
- rusticus, Omphalius