- Sabalites, genus
- Sabalites nipponicus
- Sabalites oaraiensis
- Sabal, genus
- Sabal nipponica
- Sabia, genus, Gastropods
- Sabia, genus, Plants
- Sabiaceae, family
- Saccella, genus
- Saccella confusa
- Saccella confusa kongiensis
- Saccella gordonis
- Saccella kongiensis
- Saccella konnoi
- Saccella miensis
- Saccella nagaoi
- Saccella rhombica
- Saccella saikaiensis
- Saccella sematensis
- saccharum, Acer
- Saccostrea kegaki
- sachalinensis, Abies
- sachalinensis, Fallopia
- sachalinensis, Juglans
- sachalinensis, Juglans mandshurica
- sachalinensis, Nilssonia
- sachalinensis, Reynoutria
- sachalinensis, Salix
- sachalinensis, Spisula
- Saddle oyster
- sadoensis, Betula
- sadoensis, Bibio
- sadoensis, Leda
- sadoensis, Nuculana
- sadoensis, Nuculana pernula
- sagai, Turritella
- sagamiense, Epitonium
- sagamiensis azumana, Cinctiscala
- sagamiensis, Cinctiscala
- sagamiensis, Polinices
- Sagarites, genus
- Sagarites chitanii
- Sagenopteris nariwaensis
- sagittaria, Yoldia
- saikaiensis, Saccella
- saishuensis, Turritella
- saishuensis etigoensis, Turritella
- saishuensis motidukii, Turritella
- saitamensis, Solen
- saitoi, Cornucoquimba
- Saitoum, genus
- sakaguchii, Neoschwagerina
- sakakurai, Pterotrigonia
- sakamotoi, Semisulcospira
- sakamotoi, Syringothyris
- Sakhalin fir
- Sakhalin spruce
- sakoi, Semitubina
- sakurai, Neptunea
- salicina, Prunus
- salicina, Quercus
- Salix, genus
- Salix amygdalina
- Salix bakko
- Salix gilgiana
- Salix integra
- Salix jessoensis
- Salix lackschewitziana
- Salix miyabeana supsp. gilgiana
- Salix rorida
- Salix sachalinensis
- Salix triandra
- Salix udensis
- Salmonidae, family
- Salticidae, family
- Salvinia genus
- Salvinia formosana
- Salvinia pseudoformosana
- samarangae, Keenaea
- samarangae, Nemocardium
- sambonsugii, Cancer
- sameshimai, Lima
- sanaguensis, Tulotomoides
- sanbonsugii, Populus
- sanchuensis, Amauropsis
- sanchuensis, Corbicula
- sanchuensis, Natica
- sanchuensis, Tetoria
- Sanchuryu
- sanctiioannis, Antiplanes
- sanctiioannis, Rectiplanes
- sandai, Corbicula
- Sand dollar
- Sand gaper
- sandsfootensis, Pinna
- Sand tiger shark
- sangarense, Homalopoma
- Sanguisorba, genus
- sapiens, Homo
- Sapindus, genus
- Sapindus miocenicus
- Sapium, genus
- Sapium palaeojaponicum
- Sapium sebiferum
- Sapium sebiferum var. pleistoceaca
- Sardinops, genus
- Sarepta, genus
- sargentii, Cerasus
- sargentii, Prunus
- Sargent's cherry
- Sasa veitchii
- Sassafras, genus
- Sassafras officinale
- Sassafras subtriloba
- satoi, Chlamys
- satoi, Mimachlamys
- satoi, Nipponamia
- satoi, Wakinosaurus
- satowi, Anadara
- satowi castellata, Anadara
- satowi, Colombiceras
- satsumi, Philadelphus
- Sauropod
- Sauropoda, infraorder
- Sawa hornbeam
- sawanensis, Quinqueloculina
- sawanensis, Sigmomorpha
- sawanensis, Sigmomorphina
- Sawara cypress
- sawatanus, Hemiprionites
- Sawtooth oak
- Saxidomus, genus
- Saxidomus purpurata
- Saxidomus purpuratus
- Saxifragaceae, family
- Saxifraga fortunei var. alpina
- Saxifraga fortunei var. incisolobata
- Saxolucina, genus
- Saxolucina khataii
- Scabiosa, genus
- scabra, Lepidocyclina
- scabra, Nephrolepidina
- Scacchinella gigantea
- Scaeochlamys squamata
- scalaris, Amphicoryna
- Scale tree
- scandens, Humulus
- Scapharca, genus
- Scapharca broughtonii
- Scapharca castellata
- Scapharca hiratai
- Scapharca kakehataensis
- Scapharca subcrenata
- Scaphechinus, genus
- Scaphechinus brevis
- Scaphechinus mirabilis
- Scaphechinus tenuis
- Scaphopod
- Scaphopoda, class
- scaphum, Nonion
- Scatopsidae, family
- Schantaricum, Buccinum
- Schaubcylindrichnus, ichnogenus
- schaumburgensis var. parvula, Nilssonia
- Schedohalysites kitakamiensis
- Schellwienella, genus
- schenckii, Stephanopyxis
- schenkii, Taeniopteris
- schenki, Podozamites
- schisticolor, Myopus
- Schizaster, genus
- Schizocythere kishinouyei
- Schizodus japonicus
- Schizophragma hydrangeoides
- Schizothaerus keenae
- schlegelii, Tomistoma
- schlumbergeri, Sigmoilina
- schlumbergeri, Sigmoilopsis
- schmidtii, Betula
- schmidti, Inoceramus
- Schmidt's birch
- schnelliana, Paphia
- Schoenoplectus tabernaemontani
- Schoenoplectus triangulatus
- Schoenoplectus triqueter
- schreberi, Brasenia
- Schubertella, genus
- Schuchertella, genus
- Schuettia annulata
- Schwagerina, genus
- Schwagerina japonica
- Schwagerina yabei
- sciadophylloides, Chengiopanax
- sciadophylloides, Eleutherococcus
- Sciadopitys, genus
- Sciaenidae, family
- Sciaridae, family
- Sciponoceras baculoide
- Scirpus, genus
- Scirpus tabernaemontani
- Scirpus triangulatus
- scissuratus, Plicifusus
- Sciuridae, family
- Scleractinia, order
- Scomber, genus
- Scomberomorus chichibu
- scrofa subsp. leucomystax, Sus
- sculptus, Auliscus
- sculptus, Eupodiscus
- scutelloides, Navicula
- Scylla ozawai
- Scylla serrata
- Sea bream
- Sea cow
- Sea monarch top shell
- Searlesia coreanica
- Searlesia fuscolabiata
- Searlesia japonica
- Searlesia modesta
- Sea turtle
- Sea urchin
- sebifera var. pleistoceaca, Triadica
- sebifera, Triadica
- sebiferum var. pleistoceaca, Sapium
- sebiferum, Sapium
- secta, Crotalocephalina
- sectior, Macoma
- sectior, Rexithaerus
- Securella carmanahensis
- Securella chitaniana
- Securella cryptolineata
- Securella postostriata
- Securella yiizukai
- Seed fern
- Seed shrimp
- Segmented worm
- Seila, genus
- Seirocrinus, genus
- Sei whale
- sejugata, Macoma
- sekiensis, Betula
- sekiensis, Tilia
- sekiensis, Ulmus
- Selaginella selaginoides
- selaginoides, Selaginella
- Selenarctos thibetanus
- sematensis, Aequipecten
- sematensis, Cryptopecten
- sematensis, Cryptopecten nux
- sematensis, Mizuhopecten tokyoensis
- sematensis, Nuculana confusa
- sematensis, Patinopecten tokyoensis
- sematensis, Saccella
- Semelangulus, genus
- Semelangulus miyatensis
- semiannulata, Pentatoma
- semiasperoides, Diplodonta
- Semicassis, genus
- semidecussata, Venerupis
- semigranosus, Donax
- seminuda, Bolivina
- seminula, Quinqueloculina
- seminulina, Sphaeroidinellopsis
- seminulum, Quinqueloculina
- Semionotiformes, order
- Semisulcospira, genus
- Semisulcospira (Biwamelania) gamoensis
- Semisulcospira gamoensis
- Semisulcospira multigranosa
- Semisulcospira sakamotoi
- semispina, Rhizosolenia
- Semitubina sakoi
- sempervirens, Sequoia
- sendaicus, Sinomastodon
- sendaiense, Cytheropteron
- sendaiensis, Laperousecythere
- senex, Trigonia
- septemlobus, Kalopanax
- septentrionalis, Cuspidaria gouldiana
- septentrionale, Dentalium
- septentrionalis, Platanus
- Septifer, genus
- Sequoia, genus
- Sequoia japonica
- Sequoia jeholensis
- Sequoia langsdorfii
- sequoianum, Taxodioxylon
- Sequoia sempervirens
- sericea, Plateumaris
- sericeus, Tapes
- serotina, Nilssonia
- Serow
- Serpentes, suborder
- Serpulidae, family
- Serpulorbis imbricatus
- serra, Hemipristis
- serrata, Fraxinus lanuginosa
- serrata, Huperzia
- serrata, Ilex
- serrata, Quercus
- serrata, Scylla
- serrata, Zelkova
- Serratina capsoides
- Serripes, genus
- Serripes fujinensis
- Serripes groenlandicus
- Serripes laperousii
- Serripes (Serripes) groenlandicus
- Serripes yokoyamai
- serrulatoides, Alnus
- setamaiensis, Taeniopteris
- setanaensis, Dentalina
- Sethocapsa, genus
- severa, Natica
- sexcarinata, Dendroxena
- sexcarinata, Xylodrepa
- Shark
- shataii, Turritella
- s-hataii, Turritella
- shibaharensis, Dosinia
- shibaharensis, Patinopecten
- shigensis, Mammuthus
- shigensis, Mammuthus paramammontheus
- Shikamaia, genus
- shikamai, Callianassa
- shikamai, Entemnotrochus
- Shikamainosorex densicingulata
- shikoensis, Trochocerithium
- shikokuensis, Falsicatenipora
- shikokuensis, Fusulina
- shikokuensis, Trochocerithium
- shimabarensis, Cervus
- shimabarensis, Cervus (Deperetia)
- shimaensis, Ringicula
- shimizui, Joumocetus
- shinanoensis, Bakevellia
- shinanoensis, Neobakevellia
- shinjiense, Clinocardium
- shinjiensis, Clinocardium
- shinoharai, Pterinella
- shinshuensis, Stegodon
- shiobarense, Cardium
- shiobarense, Clinocardium
- shiobarense, Laevicardium
- shiobarensis, Rana
- Shionodiscus oestrupii
- Shipworm
- shiragiana, Ostrya
- shiraianus, Styrax
- shiraiwensis, Lepidolina
- shiraiwensis, Lepidolina multiseptata
- shiraiwensis, Yabeina
- shirasawae, Picea
- shirasawanum, Acer
- Shirasawa's maple
- shiroiensis, Cyrena
- shiroiensis, Isodomella
- shiroiensis, Polymesoda
- shokonshaensis, Gemmula
- Shrew
- Shurabia elegans
- siakensis, Paragloborotalia
- sibirica, Alnus hirsuta
- sibirica, Ginkgoites
- sibogai, Propeamussium
- sicana, Globigerinoides
- sibirica, Mertensia
- sicana, Praeorbulina
- sicanus, Globigerinoides
- sieboldiana, Corylus
- sieboldiana subsp. hosenjiana, Juglans
- sieboldiana, Juglans
- sieboldiana, Juglans mandshurica
- sieboldianum, Acer
- sieboldianum f. microphyllum, Acer
- sieboldii, Castanopsis
- sieboldii, Conasprella
- sieboldii, Conus
- sieboldii, Lutraria
- sieboldii, Malus
- sieboldii, Ostericum
- sieboldii, Populus tremula
- sieboldii, Tsuga
- sieboldii, Viburnum
- Sieboldius albardae
- Siebold's cone
- Siebold's maple
- Siebold's viburnum
- sigaramiensis, Acmaea
- sigaramiensis, Mercenaria
- sigaramiensis, Notoacmea
- sigmoidale, Pravitoceras
- Sigmoilina schlumbergeri
- Sigmoilopsis schlumbergeri
- Sigmomorpha sawanensis
- Sigmomorphina sawanensis
- Sika deer
- Siliqua, genus
- Siliqua elliptica
- Sillaginidae, family
- Sillago japonica
- Silurus, genus
- Silverberry
- Silver vine
- similis, Yoldia
- simizui, Nassarius
- simizui, Reticunassa
- simosensis, Terebratulina
- simotomensis, Panomya
- simplex, Triticites
- simplum, Parahsuum
- Sinanodelphis izumidaensis
- Sinanodonta, genus
- Sinanodonta calipygos
- Sinanodonta kobiwakoensis
- Sinanodonta lauta
- Sinanodonta ogurae
- Sinanodonta woodiana
- Sinanoense, Buccinum
- sinanoensis, Eumetopias
- sinense, Kueichouphyllum
- sinensis, Annamocarya
- sinensis, Carya
- Sinensis, Cyclina
- sinensis, Liebea
- sinensis, Mauremys
- sinensis, Ocadia
- sinensis, Pecten
- sinensis puncticulatus, Pecten
- sinensis, Trapella
- sinica, Aegosoma
- sinica, Megopis
- Sinomastodon sendaicus
- Sinomegaceroides yabei
- Sinomegaceros, genus
- Sinomegaceros kinryuensis
- Sinomegaceros yabei
- Sinonovacula constricta
- Sinonucula cyrenoides
- Sinotaia, genus
- Sinum, genus
- Sinum ineptum
- sinuosa, Ceratocyrtis
- Sinusicola yendoi
- siogamensis, Cyclocardia
- siogamensis, Venericardia
- Siphonalia, genus
- Siphonalia aspersa
- Siphonalia declivis
- Siphonalia declivis biconica
- Siphonalia fusoides
- Siphonalia makiyamai
- Siphonalia minuta
- Siphonalia modificata
- Siphonalia prespadices
- Siphonalia spadicea
- Siphonalia trochulus
- Siphonodendron, genus
- Siphonodendron martini
- Siphonodosaria lepidula
- siquijorensis, Nassarius
- siquijorensis, Zeuxis
- Siratoria, genus
- Siratoria microsiratori
- Siratoria siratoriensis
- siratoriensis, Siratoria
- Sirenia, order
- Siricidae, family
- sisymbroides, Cystophyllum
- sitkana, Littorina
- Sixgill shark
- sobrina, Lissotesta
- socialis, Pinna
- Soft-shell clam
- Softshell turtle
- Soft-stemmed bulrush
- Solamen, genus
- Solecurtus, genus
- Solecurtus divaricatus
- Solecurtus dunkeri
- Solemya, genus
- Solemya (Acharax) dalli
- Solemya (Acharax) tokunagai
- Solemya dalli
- Solemya tokunagai
- Solemyidae, family
- Solen, genus
- Solen gouldi
- Solen grandis
- Solen krusensterni
- Solenomorpha elegantissima
- Solenopora, genus
- Solenospira multicostata
- Solenotryma, genus
- Solen roseomaculatus
- Solen saitamensis
- Solen strictus
- Soletellina, genus
- Soletellina minoensis
- solida, Melosira
- Solidicorbula, genus
- Solidicorbula erythrodon
- somaensis, Latomeandra
- somaensis, Meandrarea
- Somatochlora, genus
- Somniosus, genus
- Sonneratia, genus
- sookensis, Macoma
- Sophora, genus
- Sophora miojaponica
- sorbifolia, Xanthoceras
- sorbifolium, Xanthoceras
- Sorbus, genus
- Sorbus alnifolia
- Sorbus commixta
- Sorbus gracilis
- Sorbus japonica
- Sorbus uzenensis
- sorex, Epithemia
- sorex var. gracilis, Epithemia
- Soricidae, family
- Southern Japanese hemlock
- sowerbyi, Lima
- spaculifera, Pseudophillipsia
- spadicea, Siphonalia
- spaethiana, Fraxinus
- Sparganium, genus
- Sparidae, genus
- Spatangoid
- Spatangoida, order
- spathi, Hypacanthoplites
- spatiosa, Cristaria
- spatiosa, Cristaria plicata
- speciosa, Dipsastraea
- speciosa, Favia
- speciosus, Apodemus
- spectabilis, Lucinoma
- spectabilis, Storgaardia
- speculum, Dictyocha
- speculum, Distephanus
- spengleriana, Cancellaria
- spengleriana, Sydaphera
- Spengler's nutmeg
- Sperm whale
- Sphaeroidina, genus
- Sphaeroidinella dehiscens
- Sphaeroidinellopsis seminulina
- Sphaerulina, genus
- Sphenophyllum, genus
- Sphyrnidae, family
- spicatum var. muricatum, Myriophyllum
- spicatum, Myriophyllum
- Spikenard
- Spike winter hazel
- Spinicaudata, order
- Spinner shark
- Spinotriassocampe annulata
- spinulifera, Miocidaris
- spinulosa, Prunus
- Spiny oyster
- Spiraea, genus
- Spiraea prunifolia
- spiralis, Kilinora
- Spirifer, genus
- Spiriferina, genus
- Spiriferina wakasana
- Spirifer verneuili
- Spiroloculina corrugata
- Spiroloculina hadai
- Spiroloculina lucida
- Spiroloculina manifesta
- Spiromphalus, genus
- Spiromphalus yabei
- Spisula, genus
- Spisula onnechiuria
- Spisula polynyma
- Spisula (Pseudocardium) sachalinensis
- Spisula sachalinensis
- Spisula voyi
- Spisula yokoyamai
- Spizaetus nipalensis subsp. orientalis
- splendens, Actinoptychus
- Spondias axillaris var. polymeris
- Spondylus, genus
- Spondylus anacanthus
- Spondylus decoratus
- Sponge
- Spongiomorpha, genus
- Spongodiscus biconcavus
- Spongosaturnalis bispinus
- Sporadopora, genus
- Spread-winged damselfly
- spretoides, Olivella
- Springtail
- Spruce
- Squalidae, family
- Squalodon, genus
- squamata, Chlamys
- squamata, Scaeochlamys
- Squameofavosites, genus
- squamosus, Anomalocardia
- squamosus, Anomalodiscus
- Squamularia, genus
- Squamularia asiatica
- Squamularia waageni
- Squatina, genus
- Squillaconcha, genus
- Squillidae, family
- Squirrel
- Squirrel's foot fern
- Staffella, genus
- Stag beetle
- standishii, Thuja
- Staphylinidae, family
- Starfish
- Star snail
- Stauroneis, genus
- Staurosirella lapponica
- stearnsiana, Anodontia
- stearnsii, Barbatia
- Stegodon, genus
- Stegodon akashiensis
- Stegodon aurorae
- Stegodon elephantoides
- Stegodon infrequens
- Stegodon kwantoensis
- Stegodon miensis
- Stegodon orientalis
- Stegodon protoaurorae
- Stegodon shinshuensis
- Stegodon sugiyamai
- Stegolophodon pseudolatidens
- Stegolophodon tsudai
- steigeri, Aulacosphinctoides
- Steinmanella ainuana
- Steinmanella (Yeharalla) ainuana
- stellata, Culicia
- stellata, Gavia
- Steno bredanensis
- Stenoporidium, genus
- Stenoscisma, genus
- Stephanandra incisa
- Stephania dielsiana
- Stephanodiscus, genus
- Stephanodiscus astraea
- Stephanodiscus carconensis
- Stephanodiscus hantzschii
- Stephanodiscus niagarae
- Stephanopyxis, genus
- Stephanophyllia fungulus
- Stephanopyxis schenckii
- Stereocidaris, genus
- Stereolepis, genus
- Stewartia, genus
- Stewartia monadelpha
- Stewartia pseudocamellia
- Stichocapsa, genus
- Stictodiscus hardmanianus
- Stilostomella lepidula
- stimpsoni, Mercenaria
- Stimpson's hard clam
- Stink bug
- Stoat
- stokesiana subsp. miltoni, Oulangia
- Stonefly
- Stony coral
- Storgaardia spectabilis
- Straparollus, genus
- Straparollus asanoi
- Strebloplax, genus
- Streptolathyrus, genus
- Streptorhynchus, genus
- Striarca interplicata
- Striarca symmetrica
- striata, Astarte
- striata, Atactodea
- striata, Chavania
- striata, Fulgoraria
- striata, Fulgoraria (Musashia)
- striata, Lagena
- striata, Musashia
- striata, Vertebralina
- striata, Wallucina
- Striatolamia, genus
- striatum, Gaudryceras
- striatus, Ancistrolepis
- strictus, Solen
- Strigopupa strigosa
- strigosa, Pupa
- strigosa, Strigopupa
- Striodentalium rhabdotum
- Strioterebrum, genus
- Strioterebrum japonicum
- Striped bonnet
- Striped emerald
- Stromatolite
- Stromatopora, genus
- Stromatopora delicata
- Stromatopora minoensis
- Stromatoporoid
- Stromatoporoidea, class
- Strombidae, family
- Strombus japonicus
- Strong-ribbed turritella
- Strongylocentrotus, genus
- Strophonella, genus
- Sturgeon
- stuxbergii, Fagus
- Stylidium horinjiense
- Stylidophyllum, genus
- Stylina (Convexastrea), genus
- Stylocoeniella armata
- Stylocoeniella hanzawai
- Stylophora, genus
- Stylophora pistillata
- stylorum, Cyclotella
- Styphnolobium, genus
- styraciflua, Liquidambar
- Styrax, genus
- Styrax japonicus
- Styrax laevigata
- Styrax microcarpa
- Styrax microcarpha
- Styrax obassia
- Styrax obassis
- Styrax protoobassia
- Styrax rugosa
- Styrax rugosus
- Styrax shiraianus
- suaveolens, Populus
- Suavodrillia declivis
- Subangular margarite
- subangulata, Minolia
- subarchiaci, Goniomya
- subauriformis, Etrema
- subcantiana, Anthonya
- subconica, Linguaphillipsia
- subconstricta, Zirfaea
- subcorbarica, Puzosia
- subcordata, Carpinus
- subcordiformis, Juglans
- subcrenata, Anadara
- subcrenata, Scapharca
- subcrenulata, Odontopteris
- subfirma, Alnus
- subglobosa, Cassidulina
- subglobosa, Globocassidulina
- subgranulosum, Elphidium
- subhariotoidea, Amphidonte
- subincertum, Elphidium
- sublimbata, Cassidulina
- submirabilis, Acila
- subnipponica, Venericardia
- subovata, Nipponithyris
- subparvifolia, Ulmus
- subpictum, Acer
- subpyrum, Cymatium
- subquadratum, Polyptychoceras
- subramosum, Clisiophyllum
- subramosum, Hypophylloceras
- subramosum, Neophylloceras
- subrotunda, Pseudotsuga
- subrufum, Oiceoptoma
- subsenecta, Astarte
- subsuchiense, Suchium
- subsuchiense, Umbonium
- subtriloba, Sassafras
- subvariabilis, Quercus
- subyedoensis, Carpinus
- suchiense subsuchiense, Umbonium
- suchiense suchiense, Umbonium
- suchiense, Suchium
- suchiense, Umbonium
- Suchium, genus
- Suchium akitanum
- Suchium costatum
- Suchium moniliferum
- Suchium mysticum
- Suchium subsuchiense
- Suchium suchiense
- suessi, Enteletes
- Sugar maple
- sugiyamai, Favosites forbesi
- sugiyamai, Parastegodon
- sugiyamai, Stegodon
- suketoensis, Dosinia
- suketoensis, Phacosoma
- sulcata, Gaillonella
- sulcata, Melosira
- sulcataria, Mactra
- Sumatrina, genus
- sumiyagura, Trigonia
- Sunetta, genus
- superficialis, Psammocora
- superstes, Letepsammia
- Surirella, genus
- Sus, genus
- susensis, Procolpochelys?
- Sus lydekkeri
- Sus scrofa subsp. leucomystax
- sutneri, Anapachydiscus
- sutneri, Menuites
- suzuensis, Myadora
- suzukii, Bellamya
- suzukii var. fujimotoi, Tosapecten
- suzukii, Futabasaurus
- suzukii var. inflatus, Tosapecten
- suzukii subsp. suzukii, Tosapecten
- suzukii, Tosapecten suzukii