| Monument | Municipality | Comments | Image | Coordinates | Type | Ref. | 
  | Tsushima Yamaneko Prionailurus bengalensis euptilurus
 ツシマヤマネコ
 Tsushima yamaneko
 | Tsushima |  |  | 34°12′N 129°14′E / 34.20°N 129.24°E / 34.20; 129.24 (Tsushima Yamaneko) | 1.1 | [1] | 
  | Tsushima Marten Martes melampus tsuensis
 ツシマテン
 Tsushima ten
 | Tsushima |  |  | 34°12′N 129°14′E / 34.20°N 129.24°E / 34.20; 129.24 (Tsushima Marten) | 1.1 | [2] | 
  | Japanese Dormouse Glirulus japonicus
 ヤマネ
 Yamane
 |  |  |  |  | 1.1 | [3] | 
  | Japanese Wood Pigeon Columba janthina
 カラスバト
 Karasubato
 |  |  |  |  | 1.2 | [4] | 
  | Ajika-jima 阿値賀島
 Ajika-jima
 | Hirado |  |  | 33°15′02″N 129°20′21″E / 33.25054°N 129.33930°E / 33.25054; 129.33930 (Ajika-jima) |  | [5] | 
  | Ikenohara Kyushu Azalea Communities Rhododendron kiusianum
 池の原ミヤマキリシマ群落
 Ikenohara miyama kirishima gunraku
 | Unzen |  |  | 32°44′41″N 130°16′09″E / 32.74474°N 130.26920°E / 32.74474; 130.26920 (Ikenohara Kyushu Azalea Communities) | 2.4 | [6] | 
  | Isahaya City Castle Mountain Temperate Verdure 諫早市城山暖地性樹叢
 Isahaya-shi shiroyama danchi seijusō
 | Isahaya |  |  | 32°50′43″N 130°02′51″E / 32.84519°N 130.04740°E / 32.84519; 130.04740 (Isahaya City Castle Mountain Temperate Verdure) | 2.2 | [7] | 
  | Mount Iwato Verdure 岩戸山樹叢
 Iwato-yama jusō
 | Minamishimabara |  |  | 32°37′30″N 130°09′22″E / 32.62488°N 130.15600°E / 32.62488; 130.15600 (Mount Iwato Verdure) | 2.2 | [8] | 
  | Giant Mottled Eel Habitat Anguilla marmorata
 オオウナギ生息地
 Ōunagi seisokuchi
 | Nagasaki |  |  | 32°33′46″N 129°47′00″E / 32.56267°N 129.78320°E / 32.56267; 129.78320 (Giant Mottled Eel Habitat) | 1.3 | [9] | 
  | Ōmura Jinja Ōmura Cherry Prunus
 大村神社のオオムラザクラ
 Ōmura Jinja no Ōmura-zakura
 | Ōmura |  |  | 32°53′52″N 129°57′26″E / 32.89766°N 129.95720°E / 32.89766; 129.95720 (Ōmura Jinja Ōmura Cherry) | 2.1 | [10] | 
  | Ōmura Red-bark Oak Natural Forest Quercus gilva
 大村のイチイガシ天然林
 Ōmura no ichiigashi tennen-rin
 | Ōmura |  |  | 32°56′22″N 130°00′00″E / 32.93956°N 130.00000°E / 32.93956; 130.00000 (Ōmura Red-bark Oak Natural Forest) | 2.2 | [11] | 
  | Ohashi Kannon Fern Plant Communities Pteridopsida
 御橋観音シダ植物群落
 Ohashi Kannon shida shokubutsu gunraku
 | Sasebo |  |  | 33°16′22″N 129°42′04″E / 33.27273°N 129.70110°E / 33.27273; 129.70110 (Ohashi Kannon Fern Plant Communities) | 2.9,10 | [12] | 
  | Balanophora tobiracola Native Northern Limit キイレツチトリモチ自生北限地
 Kiiretsuchitorimochi jisei hoku genchi
 | Nagasaki |  |  | 32°45′21″N 129°54′09″E / 32.75585°N 129.90250°E / 32.75585; 129.90250 (Balanophora tobiracola Native Northern Limit) | 2.10 | [13] | 
  | Kuroko-jima Primeval Forest 黒子島原始林
 Kuroko-jima genshi-rin
 | Hirado |  | .jpg) | 33°22′24″N 129°33′43″E / 33.37334°N 129.56200°E / 33.37334; 129.56200 (Kuroko-jima Primeval Forest) | 2.2 | [14] | 
  | Gensei-numa Marshland Plant Communities 原生沼沼野植物群落
 Gensei-numa shōya shokubutsu gunraku
 | Unzen |  |  | 32°44′26″N 130°15′30″E / 32.74047°N 130.25830°E / 32.74047; 130.25830 (Gensei-numa Marshland Plant Communities) | 2.6 | [15] | 
  | Konagai Magnolia compressa 小長井のオガタマノキ
 Konagai no ogatamanoki
 | Isahaya |  |  | 32°55′57″N 130°09′08″E / 32.93254°N 130.15230°E / 32.93254; 130.15230 (Konagai Magnolia compressa) | 2.1 | [16] | 
  | Jigoku Zone Enkianthus cernuus Communities 地獄地帯シロドウダン群落
 Jigoku chitai shirodoudan gunraku
 | Unzen |  |  | 32°44′26″N 130°15′51″E / 32.74053°N 130.26410°E / 32.74053; 130.26410 (Jigoku Zone Enkianthus cernuus Communities) | 2.2 | [17] | 
  | Mount Sumoshira Primeval Forest 洲藻白岳原始林
 Sumoshira-take genshi-rin
 | Tsushima |  |  | 34°15′40″N 129°15′07″E / 34.26121°N 129.25190°E / 34.26121; 129.25190 (Mount Sumoshira Primeval Forest) | 2.2 | [18] | 
  | Tatsunoshima Coastal Plant Communities 辰の島海浜植物群落
 Tatsunoshima kaihin shokubutsu gunraku
 | Iki |  |  | 33°52′02″N 129°40′40″E / 33.86734°N 129.67790°E / 33.86734; 129.67790 (Tatsunoshima Coastal Plant Communities) | 2.5 | [19] | 
  | Mount Tatera Primeval Forest 龍良山原始林
 Tatera-yama genshi-rin
 | Tsushima |  |  | 34°08′31″N 129°13′33″E / 34.14204°N 129.22590°E / 34.14204; 129.22590 (Mount Tatera Primeval Forest) | 2.2 | [20] | 
  | Mount Tara Rhododendron japonoheptamerum Grouping 多良岳ツクシシャクナゲ群叢
 Tara-dake tsukushi shakunage gunsō
 | Isahaya |  | .jpg) | 32°57′58″N 130°05′24″E / 32.96616°N 130.09000°E / 32.96616; 130.09000 (Mount Tara Rhododendron japonoheptamerum Grouping) | 2.2 | [21] | 
  | Danjo Islands 男女群島
 Danjo-guntō
 | Gotō |  |  | 31°59′16″N 128°20′54″E / 31.9877°N 128.3484°E / 31.9877; 128.3484 (Danjo Islands) |  | [22] | 
  | Nanatsugama Limestone Cave 七釜鍾乳洞
 Nanatsugama shōnyūdō
 | Saikai |  |  | 33°01′32″N 129°39′44″E / 33.02542°N 129.66230°E / 33.02542; 129.66230 (Nanatsugama Limestone Cave) | 3.6 | [23] | 
  | Narao Sea Fig Ficus superba
 奈良尾のアコウ
 Narao no akō
 | Shin-Kamigotō |  |  | 32°50′23″N 129°03′35″E / 32.8398°N 129.0597°E / 32.8398; 129.0597 (Narao Sea Fig) | 2.1 | [24] | 
  | Naru Island Mount Gongen Verdure Ficus superba
 奈留島権現山樹叢
 Narushima Gongen-yama jusō
 | Gotō |  |  | 32°49′32″N 128°56′19″E / 32.82561°N 128.93850°E / 32.82561; 128.93850 (Naru Island Mount Gongen Verdure) | 2.2 | [25] | 
  | Mount No Japanese Holly Communities Ilex crenata
 野岳イヌツゲ群落
 No-dake inutsuge gunraku
 | Unzen |  |  | 32°44′38″N 130°17′20″E / 32.74402°N 130.28900°E / 32.74402; 130.28900 (Mount No Japanese Holly Communities) | 2.2 | [26] | 
  | Hijikuro River Nemalionopsis tortuosa Site of Incidence 土黒川のオキチモズク発生地
 Hijikuro-gawa no okichimozuku hassei-chi
 | Unzen |  |  | 32°50′53″N 130°17′37″E / 32.84814°N 130.29360°E / 32.84814; 130.29360 (Hijikuro River Nemalionopsis tortuosa Site of Incidence) | 2.8 | [27] | 
  | Hirado Conglomerate Rock Plant Communities 平戸礫岩の岩石地植物群落
 Hirado tsubute-iwa no ganseki-chi shokubutsu gunraku
 | Hirado |  |  | 33°14′09″N 129°23′59″E / 33.23594°N 129.39980°E / 33.23594; 129.39980 (Hirado Conglomerate Rock Plant Communities) | 2.3,10 | [28] | 
  | Fugen-dake Autumn Colour Forest 普賢岳紅葉樹林
 Fugen-dake kōyō jurin
 | Unzen |  |  | 32°45′36″N 130°17′42″E / 32.75992°N 130.29510°E / 32.75992; 130.29510 (Fugen-dake Autumn Colour Forest) | 2.2 | [29] | 
  | Heisei Shinzan 平成新山
 Heisei-shinzan
 | Shimabara, Unzen |  |  | 32°45′41″N 130°17′56″E / 32.76139°N 130.29880°E / 32.76139; 130.29880 (Heisei Shinzan) | 3.10 | [30] | 
  | Madara Island Pothole 斑島玉石甌穴
 Madara-jima tamaishi ōketsu
 | Ojika |  |  | 33°12′45″N 129°01′29″E / 33.21241°N 129.02460°E / 33.21241; 129.02460 (Madara Island Pothole) | 3.9 | [31] | 
  | Mitake Bird Breeding Grounds 御岳鳥類繁殖地
 Mitake chōrui hanshoku-chi
 | Tsushima |  |  | 34°34′17″N 129°22′44″E / 34.57126°N 129.37880°E / 34.57126; 129.37880 (Mitake Bird Breeding Grounds) | 1.2 | [32] | 
  | Meotoki Giant Japanese Cedar Cryptomeria japonica
 女夫木の大スギ
 Meotoki no ō-sugi
 | Isahaya |  |  | 32°48′59″N 130°04′00″E / 32.81639°N 130.06680°E / 32.81639; 130.06680 (Meotoki Giant Japanese Cedar) | 2.1 | [33] | 
  | Waniura Chinese Fringetree Native Spot Chionanthus retusus
 鰐浦ヒトツバタゴ自生地
 Waniura hitotsubatago jisei-chi
 | Tsushima |  |  | 34°41′22″N 129°26′32″E / 34.68946°N 129.44220°E / 34.68946; 129.44220 (Waniura Chinese Fringetree Native Spot) | 2.10 | [34] | 
  | Cyathea spinulosa Northern Native Range ヘゴ自生北限地帯
 Hego jisei hoku genchi-tai
 | Gotō |  |  | 32°39′43″N 128°46′45″E / 32.66186°N 128.77922°E / 32.66186; 128.77922 (Cyathea spinulosa Northern Native Range) | 2.10 | [35] |