- labradorica, Nonionellina
- Lacertilia, suborder
- laciniata, Ulmus
- lackschewitziana, Salix
- lacrymalis, Cynarina
- lactuca japonica, Pectinia
- lactuca japonica, Tridacophyllia
- lactuca, Pectinia
- lacustris, Coscinodiscus
- Ladinocampe japonica
- Laevicardium, genus
- Laevicardium angustum
- Laevicardium shiobarense
- Laevicardium (Trachycardium) angustum
- Laevicardium yoshidense
- Laevicaudata, order
- Laevichlamys cuneata
- Laevidentalium, genus
- laevigata, Styrax
- Laeviscala, subgenus
- laevis, Lagena
- laevis, Pourthiaea villosa
- laevis, Reussoolina
- Laganidae, family
- Lagena, genus
- Lagena alticostata
- Lagena laevis
- Lagena striata
- Lagenonodosaria fukushimaensis
- lamarckii, Meretrix
- Lamna, genus
- Lampadena nanae
- lampas, Charonia
- Lamprey
- Lamprotula, genus
- Lamp shell
- lamyi, Wallucina
- Lanceolaria, genus
- lanceolata, Achnanthes
- lanceolata, Beedeina
- lanceolata, Cymbella
- lanceolata, Frustulia
- lanceolata, Taeniopteris
- lanceolata, Tanakia
- lanceolatum, Achnanthidium lanceolatum
- lanceolatum, Cinnamomum
- lanceolatum f. lanceolatum, Achnanthidium
- lanceolatus, Podozamites
- lancifolia, Actinodaphne
- langsdorfii, Sequoia
- Lanternfish
- lanuginosa, Fraxinus
- lanuginosa f. serrata, Fraxinus
- Laperousecythere, genus
- Laperousecythere sendaiensis
- laperousii, Serripes
- lapponica, Fragilaria
- lapponica, Staurosirella
- Laqueus, genus
- Laqueus rubellus
- Larch
- larga, Gifuelloides
- Large Japanese field mouse
- Large star coral
- Larix, genus
- Larix gmelinii
- Larix gmelinii subsp. japonica
- Larix kaempferi
- Larix leptolepis
- Lasius, genus
- lata, Theora
- latecostata, Taeniopteris
- lateralis, Echinauris
- Laternula, genus
- latibracteata, Picea
- latior, Populus
- Latiproetus biloba
- Latirulus, genus
- Latomeandra, genus
- Latomeandra somaensis
- Latona cuneata
- latreillei, Macrophthalmus
- latreillei, Venitus
- Latticed top shell
- latus, Acanthopagrus
- laudabilis, Yoldia
- Lauraceae, family
- Laurel
- Laurus, genus
- lauta, Sinanodonta
- laxata, Cyclocardia
- laxiflora, Carpinus
- Laxtorum jurassicum
- Leaf beetle
- Leda, genus
- Leda sadoensis
- Legume
- lenticularis, Orbitolina
- Lenticulina, genus
- Lenticulina nikobarensis
- Lenticulina rotulata
- Leochlamys tanassevitschi
- Leopard
- Leperditia japonica
- Lapidobalanopsis, subgenus
- Lepidocyclina, genus
- Lepidocyclina japonica
- Lepidocyclina (Nephrolepidina), subgenus
- Lepidocyclina (Nephrolepidina) japonica
- Lepidocyclina (Nephrolepidina) nipponica
- Lepidocyclina nipponica
- Lepidocyclina scabra
- Lepidodendron, genus
- Lepidodesma, genus
- Lepidolina, genus
- Lepidolina multiseptata
- Lepidolina multiseptata shiraiwensis
- Lepidolina shiraiwensis
- Lepidopleurus, genus
- Lepidopleurus morozakiensis
- Lepidopsetta mochigarei
- Lepidozona, genus
- lepidula, Siphonodosaria
- lepidula, Stilostomella
- Leporidae, family
- Leporimetis takaii
- Leptastrea purpurea
- Leptobison hanaizumiensis
- Leptochondria, genus
- Leptodesma, genus
- Leptodus, genus
- Leptodus richthofeni
- leptolepis, Larix
- Leptophloeum rhombicum
- Leptoseris minikoiensis
- Leptoseris mycetoseroides
- Leptothyra amussitata
- Lepus, genus
- Lepus brachyurus subsp. angustidens
- Lesser clubmoss
- Lesser Japanese mole
- lessonii, Amphistegina
- Lesticus, genus
- Lestidae, family
- Letepsammia japonica
- Letepsammia superstes
- Lethenteron, genus
- leucogenys, Petaurista
- leucomystax, Sus scrofa
- Leucosia, genus
- Leucosiidae, family
- leucostoma, Buccinum
- Leucosyrinx yonegafukuroensis
- Leucotina, genus
- Leucotina casta
- Leucotina dianae
- Leucotina gigantea
- leucurus kuzuüensis, Meles
- Leukoma, genus
- Leukoma euglypta
- Leukoma itoigawae
- Leukoma jedoensis
- Leukoma tateiwai
- leveilleana, Prunus
- Libellulidae, family
- Libocedrus notoensis
- Liebea sinensis
- ligniatum, Acer rubrum
- Ligustrum, genus
- Ligustrum tschonoskii
- Liliaceae, family
- Lima, genus
- Lima (Acesta), genus
- lima, Barbatia
- Limacina, genus
- Lima fujitai
- Lima goliath
- Lima konnoi
- Lima naumanni
- Limanda, genus
- Limaria hakodatensis
- Lima sameshimai
- Lima sowerbyi
- Limatula, genus
- Limatula vladivostokensis
- Lima vulgaris
- Lima yagenensis
- Lima zushiensis
- Limidae, family
- Limonia quadrimaculata
- Limonia (Metalimnobia) quadrimaculata
- Limoniidae, family
- Limoniid crane fly
- Limopsis, genus
- Limopsis adamsiana
- Limopsis azumana
- Limopsis osawanoensis
- Limopsis tajimae
- Limopsis tokaiensis
- Limopsis tokaiensis elongata
- Limopsis uwadokoi
- limpida, Odostomia
- Lindera membranacea
- Lindera obtusiloba
- Lindera praecox
- Lindera protopraecox
- Lindera umbellata
- Lindera umbellata var. membranaceae
- lindleyana, Baiera
- linearis, Diatoma vulgare
- linearis, Diatoma vulgaris
- linearis, Pinnularia gibba
- lineatus, Apogon
- lineatus, Coscinodiscus
- lineolatus, Pitar
- Linguaphillipsia subconica
- Lingula, genus
- Lingula anatina
- Lingula ungius
- Lingulidae, family
- Linoproductus, genus
- Linthia, genus
- Linthia nipponica
- Linthia tokunagai
- Linuparus, genus
- Linuparus japonicus
- Liocyma, genus
- Liocyma fluctuosa
- Liocyma fluctuosum
- Liocyma furtiva
- Liocyma minuta
- Liomesus, genus
- Liquidambar, genus
- Liquidambar formosana
- Liquidambar formosana cordata
- Liquidambar miosinica
- Liquidambar styraciflua
- Liquidambar yabei
- Lirabuccinum fuscolabiatum
- Liracassis, genus
- Liralucina plicatula
- liratum, Neotrapezium
- Liriodendron, genus
- Liriodendron honsyuensis
- Lischkeia, genus
- Lischkeia crumpii
- lischkei, Anomia
- lischkei, Megayoldia
- lischkei, Mitrella
- lischkei, Nitidotellina
- lischkei, Portlandia
- lischkei, Yoldia
- Lissotesta sobrina
- Lithacoceras, genus
- Lithophaga, genus
- Lithophyllon elegans
- Lithophyllon mushroom hard coral
- Lithophyllon undulatum
- Lithophyllum, genus
- Lithophyllum nishiwadai
- Lithophyllum oborensis
- Lithostrobus, genus
- Lithostrotionella , genus
- Lithothamnium, genus
- Litseaphyllum, genus
- Little Japanese horseshoe bat
- Littoraria (Littorinopsis) miodelicatula
- Littoraria miodelicatula
- Littorina sitkana
- Littorinopsis miodelicatula
- livescens, Nassarius
- livescens, Niotha
- Lizard
- lobata, Podabacia elegans
- lobata forma vanderhorsti, Podabacia elegans
- lobatulus, Cibicides
- lobatulus, Cibicidoides
- lobatus, Zalophus
- lobatus, Zalophus californianus
- Lobed brain coral
- Lobophyllia, genus
- Lobophyllia japonica
- Lobophyllia robusta
- Longhorn beetle
- longifolia, Archaeozostera
- longifolia, Ulmus
- longifolium, Pityophyllum
- longifolium, Trochodendron aralioides
- longinux, Quercus
- Lonsdaleia, genus
- Lonsdaleoides, genus
- Lonsdaleoides toriyamai
- Lopha, genus
- Lopha diluvianum
- Lophiotoma, genus
- Lophocarinophyllum, genus
- Lophophaena, genus
- Lophophyllidium, genus
- lophos, Calappa
- lubrica, Cadella
- lubrica, Theora
- Lucanidae, family
- lucida, Spiroloculina
- Lucina acutilineata
- Lucina k-hataii
- Lucinidae, family
- Lucinoma, genus
- Lucinoma actilineata
- Lucinoma acutilineata
- Lucinoma acutilineatum
- Lucinoma annulata
- Lucinoma columbiana
- Lucinoma concentricum
- Lucinoma hannibali
- Lucinoma katayosensis
- Lucinoma mochizukii
- Lucinoma otukai
- Lucinoma spectabilis
- Lucinoma tomitensis
- luehdorfi, Bathytoma
- luhdorfi, Micantapex
- Lunatia, genus
- Lunatia pila ovata
- lunatus, Repomucenus
- Lunella, genus
- Lunella coronata correensis
- Lunella correensis
- Lunella granulata
- Lunella kurodai
- lunulata, Cyclina
- lupus, Canis
- lupus subsp. hodophilax, Canis
- lusoria, Meretrix
- luteostoma, Tonna
- lutosa, Babylonia
- Lutraria maxima
- Lutraria nenokamiensis
- Lutraria sieboldii
- luxuriosa, Acalolepta
- Luzula plumosa