# List of Special Places of Scenic Beauty, Special Historic Sites and Special Natural Monuments

To protect Japan's cultural heritage, the country's government selects through the Agency for Cultural Affairs important items and designates them as Cultural Properties under the Law for the Protection of Cultural Properties. Designated items are classified in a number of categories, one of which is Monuments(記念物, kinenbutsu). This category includes historic locations such as shell mounds, ancient tombs, sites of palaces, sites of forts or castles, monumental dwelling houses and other sites of high historical or scientific value; gardens, bridges, gorges, mountains, and other places of great scenic beauty; and natural features such as animals, plants, and geological or mineral formations of high scientific value.
The government further designates "significant" monuments classifying them in three categories: Historic Sites (史跡, shiseki), Places of Scenic Beauty (名勝, meishō), and Natural Monuments (天然記念物, tennen kinenbutsu). Items of particularly high significance receive higher classifications: Special Historic Sites (特別史跡, tokubetsu shiseki), Special Places of Scenic Beauty (特別名勝, tokubetsu meishō), and Special Natural Monuments (特別天然記念物, tokubetsu tennen kinenbutsu) respectively. As of October 24, 2023 there are 1,040 Natural Monuments, 1895 Historic Sites, 429 Places of Scenic Beauty, 75 Special Natural Monuments, 36 Special Places of Scenic Beauty and 63 Special Historic Sites.
Since a single item can fall under more than one of these categories, the total number of sites is less than the sum of designations.

## Criteria

The Agency for Cultural Affairs designates monuments based on a number of criteria. A monument can be designated based on more than one of these criteria:

### Places of Scenic Beauty and Special Places of Scenic Beauty

* Parks and gardens
* Bridges and embankments
* Flowering trees, flowering grass, autumn colors, green trees and other places of dense growth
* Places inhabited by birds and wild animals, fish/insects and others
* Rocks, caves
* Ravines, gorges, waterfalls, mountain streams, abysses
* Lakes, marshes, wetlands, floating islands, springs
* Sand dunes, spits, seasides, islands
* Volcanoes, onsen
* Mountains, hills, plateaus, plains, rivers
* Viewpoints

### Historic Sites and Special Historic Sites

* Shell mounds, settlement ruins, kofun, other historic ruins of this type
* Ruins of fortified towns, castles, government administration offices, old battlefields and other historic ruins related to politics or government
* Remains of shrines and temples, former compound grounds and other historic ruins related to religion
* Schools, research institutions, cultural facilities and other historic ruins related to education, learning or culture
* Medical care and welfare facilities, life related institution, other society and life related historic ruins
* Transport and communication facilities, forest conservation and flood control facilities, manufacture facilities and other historic sites related to finance or manufacture activities
* Graves and stone monuments with inscriptions
* Former residences, gardens, ponds and other areas of particular historical significance
* Ruins related to foreign countries or foreigners

### Natural Monuments and Special Natural Monuments

* Animals
** Well-known animals peculiar to Japan and their habitat
** Animals which are not peculiar to Japan, but need to be preserved as well-known characteristic Japanese animals, and their habitat
** Animals or animal groups peculiar to Japan within their natural environment
** Domestic animals peculiar to Japan
** Well-known imported animals presently in a wild state, with the exception of domestic animals; their habitat
** Particularly valuable animal specimen
* Plants, vegetation
** Old trees of historic interest, gigantic trees, old trees, deformed trees, cultivated pulpwood, roadside trees, shrine forests
** Representative primeval forests, rare forest flora
** Representative alpine plants, special clusters of plants on rock ground
** Representative clusters of waste land plants
** Representative examples of coastal and sand ground vegetation
** Representative examples of areas of peat forming plants
** Clusters of plants growing in caves or grottoes
** Rare water plants in garden ponds, onsen, lakes, marshes, streams, sea, etc.; algae, moss, microbes, etc.
** Remarkable occurrence of epiphytic plants on rocks, trees or shrubs
** Remarkable plant growth on marginal land
** Remarkable growth in the wild of crop plants
** Wild habitat of rare or near extinct plants
* Geological and mineralogical features
** Rocks, mineral and fossil producing sites
** Conformable and unconformable strata
** Fold and thrust strata
** Geological features caused by the work of living creatures
** Phenomena related to earthquake dislocation and landmass motion
** Caves, grottoes
** Examples of rock organization
** Onsen and their sediments
** Erosion and weathering related phenomena
** Fumaroles and other items related to volcanic activity
** Ice and frost related phenomena
** Particularly precious rock, mineral and fossil specimen
* Representative territories rich in natural monuments to be protected (Natural Protected Areas)

## Usage

The table's columns (except for Remarks and Photo) are sortable pressing the arrows symbols. The following gives an overview of what is included in the table and how the sorting works.
* Name: name of the monument as registered in the Database of Cultural Properties
* Special Place of Scenic Beauty: criteria under which the monument has been designated or "-" if it is not a Special Place of Scenic Beauty
* Special Historic Site: criteria under which the monument has been designated or "-" if it is not a Special Historic Site
* Special Natural Monument: criteria under which the monument has been designated or "-" if it is not a Special Natural Monument
* Remarks: general remarks
* Location: "town-name prefecture-name" and geo coordinates of the monument if applicable
      * sorts as "prefecture-name town-name"
* Photo: picture of the monument

## Special Places of Scenic Beauty, Special Historic Sites, Special Natural Monuments

| Name | Special Place of Scenic Beauty | Special Historic Site | Special Natural Monument | Remarks | Location |
| Mōtsū-ji garden (毛越寺庭園, mōtsūji teien) | 1 | — | — | | Iwate HiraizumiHiraizumi, Iwate 38°59′16.31″N 141°6′28.98″E﻿ / ﻿38.9878639°N 141.1080500°E﻿ / 38.9878639; 141.1080500 |
| Matsushima (松島) | 8, 11 | — | — | One of the Three Views of Japan | Miyagi variousShiogama, Shichigahama, Rifu, Matsushima, Higashimatsushima, Miyagi 38°21′59.13″N 141°4′27.87″E﻿ / ﻿38.3664250°N 141.0744083°E﻿ / 38.3664250; 141.0744083 |
| Hamarikyu Gardens (旧浜離宮庭園, kyū hamarikyū teien) | 1 | 2,8 | — | | Tokyo TokyoTokyo 35°39′35.3″N 139°45′46.5″E﻿ / ﻿35.659806°N 139.762917°E﻿ / 35.659806; 139.762917 |
| Koishikawa Kōrakuen Garden (小石川後楽園, koishikawa kōrakuen) | 1 | 8 | — | | Tokyo TokyoTokyo 35°42′19.63″N 139°44′57.37″E﻿ / ﻿35.7054528°N 139.7492694°E﻿ / 35.7054528; 139.7492694 |
| Rikugi-en (六義園) | 1 | — | — | | Tokyo TokyoTokyo 35°43′58.66″N 139°44′47.48″E﻿ / ﻿35.7329611°N 139.7465222°E﻿ / 35.7329611; 139.7465222 |
| Kurobe Gorge with Sarutobi Gorge and Mount Okukane (黒部峡谷　附　猿飛ならびに奥鐘山, kurobekyōkoku tsuketari sarutobi narabini okukaneyama) | 6 | — | 4 | | Toyama variousTateyama, Kurobe, Toyama 36°37′23.18″N 137°41′11.4″E﻿ / ﻿36.6231056°N 137.686500°E﻿ / 36.6231056; 137.686500 |
| Kenroku-en (兼六園) | 1 | — | — | One of the Three Great Gardens of Japan | Ishikawa KanazawaKanazawa, Ishikawa 36°33′43.5″N 136°39′44.99″E﻿ / ﻿36.562083°N 136.6624972°E﻿ / 36.562083; 136.6624972 |
| Ichijōdani Asakura Family Gardens (一乗谷朝倉氏庭園, Ichijōdani Asakura-shi teien) | 1 | — | — | The ruins at the same site are a Special Historic Site. | Fukui FukuiFukui, Fukui 35°59′57.95″N 136°17′43.52″E﻿ / ﻿35.9994306°N 136.2954222°E﻿ / 35.9994306; 136.2954222 |
| Mitake Shōsenkyō Gorge (御嶽昇仙峡, mitake shōsenkyō) | 5, 6 | — | — | | Yamanashi variousKōfu and Kai, Yamanashi 35°44′41.64″N 138°33′59.29″E﻿ / ﻿35.7449000°N 138.5664694°E﻿ / 35.7449000; 138.5664694 |
| Kamikōchi (上高地) | 6 | — | 4 | | Nagano MatsumotoMatsumoto, Nagano 36°14′24.93″N 137°37′27.07″E﻿ / ﻿36.2402583°N 137.6241861°E﻿ / 36.2402583; 137.6241861 |
| Konchi-in Garden (金地院庭園, konchiin teien) | 1 | — | — | | Kyoto KyotoKyoto, Kyoto 35°0′38.29″N 135°47′24.02″E﻿ / ﻿35.0106361°N 135.7900056°E﻿ / 35.0106361; 135.7900056 |
| Jishō-ji (Ginkaku-ji) Garden (慈照寺（銀閣寺）庭園, jishō-ji (ginkaku-ji) teien) | 1 | 8 | — | | Kyoto KyotoKyoto, Kyoto 35°1′35.78″N 135°47′54.31″E﻿ / ﻿35.0266056°N 135.7984194°E﻿ / 35.0266056; 135.7984194 |
| Rokuon-ji (Kinkaku-ji) Garden (鹿苑寺（金閣寺）庭園, rokuon-ji (kinkaku-ji) teien) | 1 | 8 | — | | Kyoto KyotoKyoto, Kyoto 35°2′21.38″N 135°43′43.33″E﻿ / ﻿35.0392722°N 135.7287028°E﻿ / 35.0392722; 135.7287028 |
| Jōruri-ji Garden (浄瑠璃寺庭園, jōruri-ji teien) | 1 | — | — | Also a historic site (hist-crit.: 8) | Kyoto KizugawaKizugawa, Kyoto 34°42′56.16″N 135°52′22.8″E﻿ / ﻿34.7156000°N 135.873000°E﻿ / 34.7156000; 135.873000 |
| Saihō-ji Garden (西芳寺庭園, saihō-ji teien) | 1 | — | — | Also a historic site (hist-crit.: 8) | Kyoto KyotoKyoto, Kyoto 34°59′32.5″N 135°41′3.81″E﻿ / ﻿34.992361°N 135.6843917°E﻿ / 34.992361; 135.6843917 |
| Daisen-in Shoin Garden (大仙院書院庭園, daisenin shoin teien) | 1 | — | — | Also a historic site (hist-crit.: 8) | Kyoto KyotoKyoto, Kyoto 35°2′40.66″N 135°44′45.01″E﻿ / ﻿35.0446278°N 135.7458361°E﻿ / 35.0446278; 135.7458361 |
| Daitoku-ji Hōjō Garden (大徳寺方丈庭園, daitokuji hōjō teien) | 1 | — | — | Also a historic site (hist-crit.: 8) | Kyoto KyotoKyoto, Kyoto 35°2′40.66″N 135°44′45.01″E﻿ / ﻿35.0446278°N 135.7458361°E﻿ / 35.0446278; 135.7458361 |
| Daigo-ji Sanbō-in Garden (醍醐寺三宝院庭園, daigoji sanbōin teien) | 1 | 8 | — | | Kyoto KyotoKyoto, Kyoto 34°57′6.78″N 135°49′10.2″E﻿ / ﻿34.9518833°N 135.819500°E﻿ / 34.9518833; 135.819500 |
| Amanohashidate (天橋立) | 3, 8, 11 | — | — | One of the Three Views of Japan | Kyoto MiyazuMiyazu, Kyoto 35°34′12.02″N 135°11′30.59″E﻿ / ﻿35.5700056°N 135.1918306°E﻿ / 35.5700056; 135.1918306 |
| Tenryū-ji Garden (天龍寺庭園, tenryū-ji teien) | 1 | — | — | Also a historic site (hist-crit.: 8) | Kyoto KyotoKyoto, Kyoto 35°0′56.68″N 135°40′23.53″E﻿ / ﻿35.0157444°N 135.6732028°E﻿ / 35.0157444; 135.6732028 |
| Nijō Castle Ninomaru Palace Gardens (二条城二之丸庭園, nijōjō ninomaru teien) | 1 | — | — | | Kyoto KyotoKyoto, Kyoto 35°0′48.27″N 135°44′57.22″E﻿ / ﻿35.0134083°N 135.7492278°E﻿ / 35.0134083; 135.7492278 |
| Hōkongō-in Seijo no taki waterfall and Mount Goisan (法金剛院青女滝　附　五位山, hōkongōin seijo no taki tsuketari goisan) | 1, 10 | — | — | | Kyoto KyotoKyoto, Kyoto 35°1′11.77″N 135°42′59.03″E﻿ / ﻿35.0199361°N 135.7163972°E﻿ / 35.0199361; 135.7163972 |
| Hongan-ji Ōshoin Garden (本願寺大書院庭園, honganji ōshoin teien) | 1 | — | — | Also a historic site (hist-crit: 8) | Kyoto KyotoKyoto, Kyoto 34°59′27.37″N 135°45′4.47″E﻿ / ﻿34.9909361°N 135.7512417°E﻿ / 34.9909361; 135.7512417 |
| Ryōan-ji Hōjō Garden (龍安寺方丈庭園, ryōanji hōjō teien) | 1 | — | — | Also a historic site (hist-crit: 8) | Kyoto KyotoKyoto, Kyoto 35°2′3.81″N 135°43′5.42″E﻿ / ﻿35.0343917°N 135.7181722°E﻿ / 35.0343917; 135.7181722 |
| Garden at the Eastern Heijō Palace (平城宮東院庭園, Heijō-kyū tōin teien) | 1 | — | — | Reconstruction of an 8th-century Imperial Palace Garden with ponds and pebble shore | Nara NaraNara, Nara 34°41′28″N 135°47′44″E﻿ / ﻿34.69111°N 135.79556°E﻿ / 34.69111; 135.79556 |
| Heijō-kyō Sakyō Sanjō Nibō Palace Garden (平城京左京三条二坊宮跡庭園, heijōkyō sakyō sanjō nibō miyaato teien) | 1 | 2, 8 | — | The ruins at the same site are a Special Historic Site. | Nara NaraNara, Nara 34°41′1.45″N 135°48′8.44″E﻿ / ﻿34.6837361°N 135.8023444°E﻿ / 34.6837361; 135.8023444 |
| Okayama Kōraku-en (岡山後楽園, okayama kōrakuen) | 1 | — | — | One of the Three Great Gardens of Japan | Okayama OkayamaOkayama, Okayama 34°40′3.94″N 133°56′7.78″E﻿ / ﻿34.6677611°N 133.9354944°E﻿ / 34.6677611; 133.9354944 |
| Itsukushima (厳島) | 8 | 2,3 | — | Includes one of the Three Views of Japan | Hiroshima HatsukaichiHatsukaichi, Hiroshima 34°17′1.99″N 132°19′5.9″E﻿ / ﻿34.2838861°N 132.318306°E﻿ / 34.2838861; 132.318306 |
| Sandan-kyō ravine (三段峡, sandan-kyō) | 3,5,6 | — | — | | Hiroshima AkiotaAkiōta, Hiroshima 34°37′28.85″N 132°11′8.97″E﻿ / ﻿34.6246806°N 132.1858250°E﻿ / 34.6246806; 132.1858250 |
| Ritsurin Garden (栗林公園, ritsurin kōen) | 1 | — | — | | Kagawa TakamatsuTakamatsu, Kagawa 34°19′39.2″N 134°2′35.76″E﻿ / ﻿34.327556°N 134.0432667°E﻿ / 34.327556; 134.0432667 |
| Nijinomatsubara (虹の松原) | 3,9 | — | — | | Saga KaratsuKaratsu, Saga 33°26′35.99″N 130°0′34.37″E﻿ / ﻿33.4433306°N 130.0095472°E﻿ / 33.4433306; 130.0095472 |
| Mount Unzen (雲仙岳, unzendake) | 1, 3, 9, 10 | — | — | | Nagasaki ShimabaraShimabara, Nagasaki 32°45′37.54″N 130°17′31.25″E﻿ / ﻿32.7604278°N 130.2920139°E﻿ / 32.7604278; 130.2920139 |
| Shikinaen Garden (識名園, shikinaen) | 1 | — | — | | Okinawa NahaNaha, Okinawa 26°12′14.1″N 127°42′55.32″E﻿ / ﻿26.203917°N 127.7153667°E﻿ / 26.203917; 127.7153667 |
| Lake Towada and Oirase Mountain Stream (十和田湖および奥入瀬渓流, towadako oyobi oirasekeiryū) | 6, 7 | — | — | Also a Natural Monument (4) | various variousTowadako, Aomori and Kosaka, Akita 40°28′23.05″N 140°52′39.67″E﻿ / ﻿40.4730694°N 140.8776861°E﻿ / 40.4730694; 140.8776861 |
| Dorohacchō Gorge (瀞八丁, dorohacchō) | 5,6 | — | — | Also a Natural Monument (3.1) | various variousKumanogawa, Wakayama, Kiwa, Mie and Totsukawa, Nara 33°52′23.24″N 135°51′27.43″E﻿ / ﻿33.8731222°N 135.8576194°E﻿ / 33.8731222; 135.8576194 |
| Mount Fuji (富士山, fujisan) | 10 | — | — | | various variousYamanashi, Shizuoka 35°21′28.8″N 138°43′51.6″E﻿ / ﻿35.358000°N 138.731000°E﻿ / 35.358000; 138.731000 |
| Goryōkaku site (五稜郭跡, goryōkakuato) | — | 2 | — | Star fort of the Republic of Ezo | Hokkaido HakodateHakodate, Hokkaidō 41°47′49.8″N 140°45′24.3″E﻿ / ﻿41.797167°N 140.756750°E﻿ / 41.797167; 140.756750 |
| Sannai-Maruyama Site (三内丸山遺跡, Sannai Maruyama iseki) | — | 1 | — | Jōmon period archaeological site | Aomori AomoriAomori, Aomori 40°48′40.24″N 140°41′44.3″E﻿ / ﻿40.8111778°N 140.695639°E﻿ / 40.8111778; 140.695639 |
| Chūson-ji compound (中尊寺境内, chūsonji keidai) | — | 3 | — | | Iwate HiraizumiHiraizumi, Iwate 39°0′6.68″N 141°6′0.46″E﻿ / ﻿39.0018556°N 141.1001278°E﻿ / 39.0018556; 141.1001278 |
| Muryōkōin site (無量光院跡, muryōkōinato) | — | 3 | — | | Iwate HiraizumiHiraizumi, Iwate 38°59′36.08″N 141°6′56.81″E﻿ / ﻿38.9933556°N 141.1157806°E﻿ / 38.9933556; 141.1157806 |
| Site of a Chinjusha attached to the Mōtsū-ji compound (毛越寺境内　附　鎮守社跡, mōtsūji keidai tsuketari chinjushaato) | — | 3 | — | | Iwate HiraizumiHiraizumi, Iwate 38°59′13.89″N 141°6′27.26″E﻿ / ﻿38.9871917°N 141.1075722°E﻿ / 38.9871917; 141.1075722 |
| Site of a temple attached to the site of the Taga Castle (多賀城跡　附　寺跡, tagajōato tsuketari teraato) | — | 2, 3 | — | | Miyagi TagajoTagajō, Miyagi 38°17′57.54″N 140°59′52.41″E﻿ / ﻿38.2993167°N 140.9978917°E﻿ / 38.2993167; 140.9978917 |
| Ōyu Stone Circle (大湯環状列石, ōyu kanjō resseki) | — | 1 | — | | Akita KazunoKazuno, Akita 40°16′16.96″N 140°48′15.06″E﻿ / ﻿40.2713778°N 140.8041833°E﻿ / 40.2713778; 140.8041833 |
| Former Kōdōkan School (旧弘道館, kyūkōdōkan) | — | 4 | — | Former school of the Mito Clan, founded in 1841 by Tokugawa Nariaki | Ibaraki MitoMito, Ibaraki 36°22′31.54″N 140°28′38.27″E﻿ / ﻿36.3754278°N 140.4772972°E﻿ / 36.3754278; 140.4772972 |
| Hitachi Kokubun-ji site (常陸国分寺跡, hitachi kokubunjiato) | — | 3 | — | | Ibaraki IshiokaIshioka, Ibaraki 36°11′48.17″N 140°16′25.38″E﻿ / ﻿36.1967139°N 140.2737167°E﻿ / 36.1967139; 140.2737167 |
| Hitachi Kokubun Nunnery site (常陸国分尼寺跡, hitachi kokubun nijiato) | — | 3 | — | | Ibaraki IshiokaIshioka, Ibaraki 36°12′6.18″N 140°16′3.25″E﻿ / ﻿36.2017167°N 140.2675694°E﻿ / 36.2017167; 140.2675694 |
| Ōya Magaibutsu (大谷磨崖仏, ōya magaibutsu) | — | 3 | — | Stone reliefs of Buddhist deities in a cave | Tochigi UtsunomiyaUtsunomiya, Tochigi 36°35′46.35″N 139°49′16.94″E﻿ / ﻿36.5962083°N 139.8213722°E﻿ / 36.5962083; 139.8213722 |
| Cedar Avenue of Nikkō and attached donation monuments (日光杉並木街道　附　並木寄進碑, nikkō suginamiki kaidō tsuketari namiki kishinhi) | — | 6 | 2.1 | Three roads totalling 37 km (23 mi) | Tochigi NikkoNikkō, Imaichi and Kanuma, Tochigi 36°35′46.35″N 139°49′16.94″E﻿ / ﻿36.5962083°N 139.8213722°E﻿ / 36.5962083; 139.8213722 |
| Kanaizawa Stele (金井沢碑, kanaizawahi) | — | 3, 7 | — | 110 cm (43 in) high stone stele from 726 | Gunma TakasakiTakasaki, Gunma 36°17′8.37″N 139°0′58.21″E﻿ / ﻿36.2856583°N 139.0161694°E﻿ / 36.2856583; 139.0161694 |
| Yamanoue stele and kofun (山上碑及び古墳, yamanouehi oyobi kofun) | — | 1, 7 | — | | Gunma TakasakiTakasaki, Gunma 36°16′37.48″N 139°1′40.09″E﻿ / ﻿36.2770778°N 139.0278028°E﻿ / 36.2770778; 139.0278028 |
| Tago Stele (多胡碑, tagohi) | — | 2, 7 | — | | Gunma TakasakiTakasaki, Gunma 36°15′54.1″N 138°59′46.67″E﻿ / ﻿36.265028°N 138.9962972°E﻿ / 36.265028; 138.9962972 |
| Edo Castle site (江戸城跡, edojōato) | — | 2 | — | | Tokyo TokyoTokyo 35°41′8.93″N 139°45′23.95″E﻿ / ﻿35.6858139°N 139.7566528°E﻿ / 35.6858139; 139.7566528 |
| Kasori Shell Mound (加曽利貝塚, Kasori Kaizuka) | — | 1 | — | Mid to late Jōmon period shell mound. Largest shell heap in Japan. | Chiba Chiba Wakaba-kuWakaba Ward, Chiba, Chiba, Chiba 35°37′24″N 140°9′53″E﻿ / ﻿35.62333°N 140.16472°E﻿ / 35.62333; 140.16472 |
| Ichijōdani Asakura Family Historic Ruins (一乗谷朝倉氏遺跡, Ichijōdani Asakura-shi iseki) | — | 2, 3, 6, 7, 8 | — | The gardens at the same site are a Special Place of Scenic Beauty. | Fukui FukuiFukui, Fukui 35°59′57.95″N 136°17′43.52″E﻿ / ﻿35.9994306°N 136.2954222°E﻿ / 35.9994306; 136.2954222 |
| Togari Ishi Stone Age ruins (尖石石器時代遺跡, togariishi sekkijidai iseki) | — | 1 | — | Jōmon period archaeological site | Nagano ChinoChino, Nagano 36°0′46.32″N 138°13′55.04″E﻿ / ﻿36.0128667°N 138.2319556°E﻿ / 36.0128667; 138.2319556 |
| Tōtomi Kokubun-ji site (遠江国分寺跡, tōtomi kokubunjiato) | — | 3 | — | | Shizuoka IwataIwata, Shizuoka 34°43′10.45″N 137°51′5.75″E﻿ / ﻿34.7195694°N 137.8515972°E﻿ / 34.7195694; 137.8515972 |
| Arai Barrier site (新居関跡, arainosekiato) | — | 6 | — | Set up by Tokugawa Ieyasu | Shizuoka AraiArai, Shizuoka 34°41′40.99″N 137°33′40.82″E﻿ / ﻿34.6947194°N 137.5613389°E﻿ / 34.6947194; 137.5613389 |
| Toro archaeological site (登呂遺跡, toro iseki) | — | 1 | — | Late Yayoi archaeological site | Shizuoka ShizuokaShizuoka, Shizuoka 34°57′22.26″N 138°24′29.74″E﻿ / ﻿34.9561833°N 138.4082611°E﻿ / 34.9561833; 138.4082611 |
| Nagoya Castle site (名古屋城跡, nagoyajōato) | — | 2 | — | | Aichi NagoyaNagoya, Aichi 35°11′5.8″N 136°53′58.77″E﻿ / ﻿35.184944°N 136.8996583°E﻿ / 35.184944; 136.8996583 |
| Former residence of Motoori Norinaga (本居宣長旧宅　同　宅跡, Motoori Norinaga kyūtaku dōtakuato) | — | 8 | — | | Mie MatsusakaMatsusaka, Mie 34°34′30.9″N 136°31′32.94″E﻿ / ﻿34.575250°N 136.5258167°E﻿ / 34.575250; 136.5258167 |
| Azuchi Castle site (安土城跡, azuchijōato) | — | 2 | — | | Shiga variousAzuchi and Higashiōmi, Shiga 35°9′21.25″N 136°8′21.79″E﻿ / ﻿35.1559028°N 136.1393861°E﻿ / 35.1559028; 136.1393861 |
| Hikone Castle site (彦根城跡, hikonejōato) | — | 2 | — | | Shiga HikoneHikone, Shiga 35°16′35.87″N 136°15′9.02″E﻿ / ﻿35.2766306°N 136.2525056°E﻿ / 35.2766306; 136.2525056 |
| Osaka Castle site (大坂城跡, osakajōato) | — | 2 | — | | Osaka OsakaOsaka, Osaka 34°41′14.3″N 135°31′35.04″E﻿ / ﻿34.687306°N 135.5264000°E﻿ / 34.687306; 135.5264000 |
| Kudara-dera site (百済寺, kuderaderaato) | — | 3 | — | | Osaka HirakataHirakata, Osaka 34°48′55.29″N 135°39′39.15″E﻿ / ﻿34.8153583°N 135.6608750°E﻿ / 34.8153583; 135.6608750 |
| Himeji Castle site (姫路城跡, himejijōato) | — | 2 | — | | Hyogo HimejiHimeji, Hyōgo 34°50′18.85″N 134°41′34.97″E﻿ / ﻿34.8385694°N 134.6930472°E﻿ / 34.8385694; 134.6930472 |
| Kitora Tomb (キトラ古墳, kitora kofun) | — | 1 | — | | Nara AsukaAsuka, Nara 34°27′5.25″N 135°48′18.49″E﻿ / ﻿34.4514583°N 135.8051361°E﻿ / 34.4514583; 135.8051361 |
| Takamatsuzuka Tomb (高松塚古墳, takamatsuzuka kofun) | — | 1 | — | | Nara AsukaAsuka, Nara 34°27′43.94″N 135°48′23.2″E﻿ / ﻿34.4622056°N 135.806444°E﻿ / 34.4622056; 135.806444 |
| Yama-dera site (山田寺跡, yamadaderaato) | — | 3 | — | | Nara SakuraiSakurai, Nara 34°29′4.02″N 135°49′48.09″E﻿ / ﻿34.4844500°N 135.8300250°E﻿ / 34.4844500; 135.8300250 |
| Ishibutai Kofun (石舞台古墳) | — | 1 | — | | Nara AsukaAsuka, Nara 34°28′0.15″N 135°49′33.88″E﻿ / ﻿34.4667083°N 135.8260778°E﻿ / 34.4667083; 135.8260778 |
| Suyama Kofun (巣山古墳) | — | 1 | — | | Nara KoryoKōryō, Nara 34°33′23.06″N 135°44′27.63″E﻿ / ﻿34.5564056°N 135.7410083°E﻿ / 34.5564056; 135.7410083 |
| Fujiwara Palace site (藤原宮跡, fujiwara kyūseki) | — | 2 | — | Palace of the Fujiwara capital | Nara KashiharaKashihara, Nara 34°30′8.71″N 135°48′26.44″E﻿ / ﻿34.5024194°N 135.8073444°E﻿ / 34.5024194; 135.8073444 |
| Monjuin Nishi Kofun (文殊院西古墳) | — | 1 | — | | Nara SakuraiSakurai, Nara 34°30′13.55″N 135°50′33.21″E﻿ / ﻿34.5037639°N 135.8425583°E﻿ / 34.5037639; 135.8425583 |
| Heijō Palace site (平城宮跡, heijō kyūseki) | — | 2 | — | Palace of the Heijō capital; the gardens at the same site are a Special Place of Scenic Beauty | Nara NaraNara, Nara 34°41′28.46″N 135°47′42.02″E﻿ / ﻿34.6912389°N 135.7950056°E﻿ / 34.6912389; 135.7950056 |
| Moto Yakushi-ji site (本薬師寺跡, motoyakushijiato) | — | 3 | — | Yakushi-ji of the Fujiwara capital | Nara KashiharaKashihara, Nara 34°29′33.88″N 135°48′0.95″E﻿ / ﻿34.4927444°N 135.8002639°E﻿ / 34.4927444; 135.8002639 |
| Iwase Senzuka Kofun Group (岩橋千塚古墳群, iwase senzuka kofungun) | — | 1 | — | | Wakayama WakayamaWakayama, Wakayama 34°13′33.08″N 135°13′38.9″E﻿ / ﻿34.2258556°N 135.227472°E﻿ / 34.2258556; 135.227472 |
| Sai no Ohai-ji site (斎尾廃寺跡, sainoohaijiato) | — | 3 | — | | Tottori TohakuTōhaku, Tottori 35°28′53.65″N 133°42′41.13″E﻿ / ﻿35.4815694°N 133.7114250°E﻿ / 35.4815694; 133.7114250 |
| Former Shizutani School with Camelia mound, stone gate, site of the residence of Tsuda Nagatada and tea house (旧閑谷学校　附　椿山石門津田永忠宅跡および黄葉亭, kyūshizutanigakkō tsuketari tsubakiyama sekimon tsudanagatadatakuato oyobi kōyōtei) | — | 4 | — | | Okayama BizenBizen, Okayama 34°47′46.77″N 134°13′10.23″E﻿ / ﻿34.7963250°N 134.2195083°E﻿ / 34.7963250; 134.2195083 |
| Renjuku Fourmer Chazan Kan house (廉塾ならびに菅茶山旧宅, renjuku narabini kansazankyūtaku) | — | 4, 8 | — | Chazan Kan (1748–1827) was a Confucian scholar. | Hiroshima FukuyamaFukuyama, Hiroshima 34°32′41.26″N 133°23′4.1″E﻿ / ﻿34.5447944°N 133.384472°E﻿ / 34.5447944; 133.384472 |
| Sanuki Kokubun-ji site (讃岐国分寺跡, sanuki kokubunjiato) | — | 3 | — | Temple 80 of the Shikoku pilgrimage | Kagawa HiraizumiTakamatsu, Kagawa 34°18′13.18″N 133°56′39.65″E﻿ / ﻿34.3036611°N 133.9443472°E﻿ / 34.3036611; 133.9443472 |
| Ōzuka Kofun (王塚古墳) | — | 1 | — | | Fukuoka KeisenKeisen, Fukuoka 33°35′19.47″N 130°39′49.84″E﻿ / ﻿33.5887417°N 130.6638444°E﻿ / 33.5887417; 130.6638444 |
| Mizuki site (水城跡, mizukiato) | — | 2 | — | Low embankment built in 664 by the Dazaifu (大宰府), the imperial office governing Kyūshū, against an invasion from Tang dynasty China and Korea | Fukuoka variousDazaifu, Kasuga and Ōnojō, Fukuoka 33°31′2.41″N 130°29′28.42″E﻿ / ﻿33.5173361°N 130.4912278°E﻿ / 33.5173361; 130.4912278 |
| Dazaifu site (大宰府跡, dazaifuato) | — | 2 | — | Ruins of the governmental office with jurisdiction over Kyūshū | Fukuoka DazaifuDazaifu, Fukuoka 33°30′52.43″N 130°30′54.55″E﻿ / ﻿33.5145639°N 130.5151528°E﻿ / 33.5145639; 130.5151528 |
| Ōnojō Castle Ruins (大野城跡, ōnojōato) | — | 2, 3 | — | Asuka period castle | Fukuoka variousDazaifu, Umi and Ōnojō, Fukuoka 33°31′16.9″N 130°30′54.01″E﻿ / ﻿33.521361°N 130.5150028°E﻿ / 33.521361; 130.5150028 |
| Yoshinogari site (吉野ヶ里遺跡, yoshinogari iseki) | — | 1 | — | Yayoi period archaeological site | Saga YoshinogariYoshinogari, Saga 33°19′25.18″N 130°23′6.43″E﻿ / ﻿33.3236611°N 130.3851194°E﻿ / 33.3236611; 130.3851194 |
| Nagoya Castle ruined foundations (名護屋城跡並陣跡, nagoyajōato narabini jinato) | — | 2 | — | | Saga variousChinzei, Yobuko and Genkai, Saga 33°31′48.65″N 129°52′9.75″E﻿ / ﻿33.5301806°N 129.8693750°E﻿ / 33.5301806; 129.8693750 |
| Kaneda Castle site (金田城跡, kanedajōato) | — | 2 | — | Asuka period mountain castle | Nagasaki TsushimaTsushima, Nagasaki 34°16′6.07″N 129°18′49.69″E﻿ / ﻿34.2683528°N 129.3138028°E﻿ / 34.2683528; 129.3138028 |
| Haru no Tsuji Site (原の辻遺跡, haru no tsujii seki) | — | 1 | — | | Nagasaki IkiIki, Nagasaki 33°45′48.68″N 129°44′55.04″E﻿ / ﻿33.7635222°N 129.7486222°E﻿ / 33.7635222; 129.7486222 |
| Kumamoto Castle site (熊本城跡, kumamotojōato) | — | 2 | — | | Kumamoto KumamotoKumamoto, Kumamoto 32°48′20.55″N 130°42′21.21″E﻿ / ﻿32.8057083°N 130.7058917°E﻿ / 32.8057083; 130.7058917 |
| Usuki Stone Buddhas with five-storied stone pagoda and two gorintō with inscriptions from 1170 and 1172 (臼杵磨崖仏 　附　日吉塔、嘉応二年在銘五輪塔 　承安二年在銘五輪塔, usuki magaibutsu tsuketari hiyoshitō kaōninenzaimei gorintō jōanninenzaimei gorintō) | — | 3 | — | | Oita UsukiUsuki, Ōita 33°5′26.18″N 131°45′47.04″E﻿ / ﻿33.0906056°N 131.7630667°E﻿ / 33.0906056; 131.7630667 |
| Saitobaru Burial Mounds (西都原古墳群, saitobaru kofun-guni) | — | 1 | — | | Miyazaki SaitoSaito, Miyazaki 32°7′14.95″N 131°23′17.84″E﻿ / ﻿32.1208194°N 131.3882889°E﻿ / 32.1208194; 131.3882889 |
| Kii Castle site (基肄（椽）城跡, kiijōato) | — | 2 | — | | variousChikushino, Fukuoka and Kiyama, Saga 33°26′39.34″N 130°30′36.09″E﻿ / ﻿33.4442611°N 130.5100250°E﻿ / 33.4442611; 130.5100250 |
| Mount Apoi alpine plant community (アポイ岳高山植物群落, apoidake kōzanshokubutsu gunraku) | — | — | 2.3 | | Hokkaido SamaniSamani, Hokkaidō 42°6′25.35″N 143°1′41.89″E﻿ / ﻿42.1070417°N 143.0283028°E﻿ / 42.1070417; 143.0283028 |
| Marimo of Lake Akan (阿寒湖のマリモ, akanko no marimo) | — | — | 2.12, 2.8 | | Hokkaido AkanAkan, Hokkaidō 43°27′1.54″N 144°5′57.93″E﻿ / ﻿43.4504278°N 144.0994250°E﻿ / 43.4504278; 144.0994250 |
| Showashinzan (昭和新山) | — | — | 3.10 | | Hokkaido SobetsuSōbetsu, Hokkaidō 42°32′37.17″N 140°51′51.77″E﻿ / ﻿42.5436583°N 140.8643806°E﻿ / 42.5436583; 140.8643806 |
| Daisetsuzan (大雪山) | — | — | 4 | | Hokkaido variousKamikawa, Higashikawa, Biei and Shintoku, Hokkaidō 43°40′58.87″N 142°53′55.78″E﻿ / ﻿43.6830194°N 142.8988278°E﻿ / 43.6830194; 142.8988278 |
| Nopporo Forest Park (野幌原始林, nopporo genshirin) | — | — | 2.2 | | Hokkaido KitahiroshimaKitahiroshima, Hokkaidō 43°3′12.46″N 141°30′3.09″E﻿ / ﻿43.0534611°N 141.5008583°E﻿ / 43.0534611; 141.5008583 |
| Swans on Kominato beach and their wintering place (小湊のハクチョウおよびその渡来地, kominato no hakuchō oyobi sono toraichi) | — | — | 1.2 | Whooper swans | Aomori HiranaiAsadokoro, Hiranai, Aomori 40°56′14.09″N 140°58′23.88″E﻿ / ﻿40.9372472°N 140.9733000°E﻿ / 40.9372472; 140.9733000 |
| Getō Onsen Tufa (夏油温泉の石灰華, getō onsen no sekkaika) | — | — | 3.8 | | Iwate KitakamiKitakami, Iwate 39°12′36.64″N 140°52′55.74″E﻿ / ﻿39.2101778°N 140.8821500°E﻿ / 39.2101778; 140.8821500 |
| Nesori petrified wood (根反の大珪化木, nesori no daikeikaboku) | — | — | 3.1 | 15–20 million years old | Iwate IchinoheIchinohe, Iwate 40°11′24.78″N 141°20′4.42″E﻿ / ﻿40.1902167°N 141.3345611°E﻿ / 40.1902167; 141.3345611 |
| Yakehashiri lava flow (焼走り熔岩流, yakehashiri yōganryū) | — | — | 3.5, 3.10 | | Iwate NishineNishine, Iwate 39°52′30.82″N 141°2′51.16″E﻿ / ﻿39.8752278°N 141.0475444°E﻿ / 39.8752278; 141.0475444 |
| Mount Hayachine and Yakushidake alpine zone, forest vegetation (早池峰山および薬師岳の高山帯・森林植物群落, hayachinesan oyobi yakushidake no kōzantai shinrin shokubutsugunraku) | — | — | 2.3 | | Iwate variousHanamaki, Tōno and Kawai, Iwate 39°31′53.71″N 141°28′26.53″E﻿ / ﻿39.5315861°N 141.4740361°E﻿ / 39.5315861; 141.4740361 |
| onikōbe no megama oyobi ogama kanketsu onsen (鬼首の雌釜および雄釜間歇温泉) | — | — | 3.8 | | Miyagi OsakiŌsaki, Miyagi 38°48′0.19″N 140°38′52.81″E﻿ / ﻿38.8000528°N 140.6480028°E﻿ / 38.8000528; 140.6480028 |
| Tamagawa Hot Spring hokutolite (玉川温泉の北投石, tamagawa onsen no hokutōseki) | — | — | 3.1, 3.8 | Hokutolite is a type of radioactive baryte. | Akita SembokuSemboku, Akita 39°57′42.57″N 140°43′42.18″E﻿ / ﻿39.9618250°N 140.7283833°E﻿ / 39.9618250; 140.7283833 |
| Mount Haguro cedar avenue (羽黒山のスギ並木, hagursan no suginamiki) | — | — | 2.1 | | Yamagata TsuruokaTsuruoka, Yamagata 38°42′13.91″N 139°58′13.33″E﻿ / ﻿38.7038639°N 139.9703694°E﻿ / 38.7038639; 139.9703694 |
| Large zelkova tree of Higashine (東根の大ケヤキ, higashine no ōkeyaki) | — | — | 2.1 | More than 1000 years old, and perimeter larger than 12 (m), largest zelkova tree in Japan | Yamagata HigashineHigashine, Yamagata 38°26′31.16″N 140°24′6.28″E﻿ / ﻿38.4419889°N 140.4017444°E﻿ / 38.4419889; 140.4017444 |
| Natural habitat Pinguicula ramosa (コウシンソウ自生地, higashine no ōkeyaki) | — | — | 2.12 | A species of butterwort endemic to Nikkō National Park | Tochigi NikkoNikkō, Tochigi 36°40′27.13″N 139°21′42.9″E﻿ / ﻿36.6742028°N 139.361917°E﻿ / 36.6742028; 139.361917 |
| Mount Asama lava tree mold (浅間山熔岩樹型, asamayama yōganjukei) | — | — | 3.2, 3.7, 3.10 | | Gunma TsumagoiTsumagoi, Gunma 36°26′53.57″N 138°30′56.25″E﻿ / ﻿36.4482139°N 138.5156250°E﻿ / 36.4482139; 138.5156250 |
| Sakitama Kofun Group (埼玉古墳群, sakitama kofungun) | — | 1 | — | A large group of kofun comprising Maruhakayama Kofun, Futagoyama Kofun, Teppōyama Kofun, Shogunyama Kofun [ja], Nakanoyama Kofun, Kawarazuka Kofun, Okunoyama Kofun, Atagoyama Kofun and Inariyama Kofun whose artifacts have been designated as National Treasure of Japan. | Saitama GyodaGyōda, Saitama 36°7′37″N 139°28′44″E﻿ / ﻿36.12694°N 139.47889°E﻿ / 36.12694; 139.47889 |
| Wisteria at Ushijima (牛島のフジ, ushijima no fuji) | — | — | 2.1 | | Saitama KasukabeKasukabe, Saitama 35°59′5.83″N 139°46′24.07″E﻿ / ﻿35.9849528°N 139.7733528°E﻿ / 35.9849528; 139.7733528 |
| Kagami-iwa rock at Mount Mitake (御獄の鏡岩, mitake no kagamiiwa) | — | — | 3.1, 3.5 | | Saitama KamikawaKamikawa, Saitama 36°10′45.91″N 139°4′14.18″E﻿ / ﻿36.1794194°N 139.0706056°E﻿ / 36.1794194; 139.0706056 |
| Tajimagahara Primula sieboldii primrose habitat (田島ヶ原サクラソウ自生地, tajimagahara sakurasō jiseichi) | — | — | 2.4 | | Saitama SaitamaSaitama, Saitama 35°50′17.41″N 139°36′56.66″E﻿ / ﻿35.8381694°N 139.6157389°E﻿ / 35.8381694; 139.6157389 |
| Tai-no-ura sea bream habitat (鯛の浦タイ生息地, tai no ura tai seisokuchi) | — | — | 1.3 | | Chiba KamogawaKamogawa, Chiba 35°7′5.98″N 140°11′28.67″E﻿ / ﻿35.1183278°N 140.1912972°E﻿ / 35.1183278; 140.1912972 |
| Ōshima cherry tree (大島のサクラ株, ōshima no sakurakabu) | — | — | 2.1 | Single tree, 7.9 m (26 ft) circumference; species is native to Ōshima and Izu Peninsula | Tokyo OshimaŌshima, Tokyo 34°45′49.01″N 139°26′3.07″E﻿ / ﻿34.7636139°N 139.4341861°E﻿ / 34.7636139; 139.4341861 |
| Firefly squid sea surface group (ホタルイカ群遊海面, hotaruika-gun yūkaimen) | — | — | 1.3 | | Toyama variousToyama and Uozu, Toyama 36°46′36.01″N 137°20′40.69″E﻿ / ﻿36.7766694°N 137.3446361°E﻿ / 36.7766694; 137.3446361 |
| Uozu buried forest (魚津埋没林, uozu maibutsurin) | — | — | 3.1, 3.5 | Tree trunks of a cedar forest partially buried about 2000 years ago; largest has a circumference of c. 12 m (39 ft) | Toyama Uozu ShakadoShakadō, Uozu, Toyama 36°49′31.5″N 137°24′23.53″E﻿ / ﻿36.825417°N 137.4065361°E﻿ / 36.825417; 137.4065361 |
| Yakushidake cirque group (薬師岳の圏谷群, yakushidake no kenkokugun) | — | — | 3.11 | | Toyama ToyamaToyama, Toyama 36°28′5.64″N 137°32′38.48″E﻿ / ﻿36.4682333°N 137.5440222°E﻿ / 36.4682333; 137.5440222 |
| Sinter cones (岩間の噴泉塔群, iwama no funsentōgun) | — | — | 3.8 | | Ishikawa HakusanHakusan, Ishikawa 36°13′39.32″N 136°46′11.69″E﻿ / ﻿36.2275889°N 136.7699139°E﻿ / 36.2275889; 136.7699139 |
| Narusawa lava tree mold (鳴沢熔岩樹型, narusawayōganjukei) | — | — | 3.6, 3.10 | | Yamanashi NarusawaNarusawa, Yamanashi 35°25′34.06″N 138°42′3.05″E﻿ / ﻿35.4261278°N 138.7008472°E﻿ / 35.4261278; 138.7008472 |
| Shirahone Onsen stalagmite and spherical limestones (白骨温泉の噴湯丘と球状石灰石, shirahone onsen no funtōkyū to kyūjōsekkaiseki) | — | — | 3.8 | | Nagano MatsumotoMatsumoto, Nagano 36°8′51.72″N 137°37′28.85″E﻿ / ﻿36.1477000°N 137.6246806°E﻿ / 36.1477000; 137.6246806 |
| Neodani Fault (根尾谷断層, neodani dansō) | — | — | 3.5 | | Gifu MotosuMotosu, Gifu 35°37′1.62″N 136°37′14.98″E﻿ / ﻿35.6171167°N 136.6208278°E﻿ / 35.6171167; 136.6208278 |
| Itoshiro cedar (石徹白のスギ, itoshiro no sugi) | — | — | 2.1 | Circumference 14 m (46 ft) | Gifu GujoGujō, Gifu 36°0′5.83″N 136°46′18.49″E﻿ / ﻿36.0016194°N 136.7718028°E﻿ / 36.0016194; 136.7718028 |
| Kariyado gebazakura (狩宿の下馬ザクラ, kariyado no gebazakura) | — | — | 2.1 | Oldest tree of the mountain sakura, crown 21.81 m (71.6 ft) (EW) and 16.33 m (53.6 ft) (NS) | Shizuoka FujinomiyaFujinomiya, Shizuoka 35°18′6.92″N 138°35′19.59″E﻿ / ﻿35.3019222°N 138.5887750°E﻿ / 35.3019222; 138.5887750 |
| Wakutama pond (湧玉池, wakutama no ike) | — | — | 3.10 | | Shizuoka FujinomiyaFujinomiya, Shizuoka 35°13′38.07″N 138°36′41.14″E﻿ / ﻿35.2272417°N 138.6114278°E﻿ / 35.2272417; 138.6114278 |
| Nagaoka fireflies and their habitat (長岡のゲンジボタルおよびその発生地, nagaoka no genjibotaru oyobi sono hassei) | — | — | 1.2 | | Shiga MaibaraMaibara, Shiga 35°21′22.54″N 136°22′4.84″E﻿ / ﻿35.3562611°N 136.3680111°E﻿ / 35.3562611; 136.3680111 |
| Kasugayama Primeval Forest (春日山原始林, kasugayama genshirin) | — | — | 2.2 | Part of the World Heritage Site "Historic Monuments of Ancient Nara" | Nara NaraNara, Nara 34°40′56.19″N 135°51′46.13″E﻿ / ﻿34.6822750°N 135.8628139°E﻿ / 34.6822750; 135.8628139 |
| Daisen agarwood single species forest (大山のダイセンキャラボク純林, daisen no daisenkyaraboku junrin) | — | — | 2.2 | | Tottori DaisenDaisen, Tottori 35°29′0.95″N 133°30′28.51″E﻿ / ﻿35.4835972°N 133.5079194°E﻿ / 35.4835972; 133.5079194 |
| Daikon Island lava tubes (大根島の熔岩隧道, daikonjima no yōganzuidō) | — | — | 3.6, 3.10 | | Shimane MatsueMatsue, Shimane 35°29′42.59″N 133°10′34.42″E﻿ / ﻿35.4951639°N 133.1762278°E﻿ / 35.4951639; 133.1762278 |
| Akiyoshi plateau (秋吉台, akiyoshidai) | — | — | 3.1, 3.3, 3.6, 3.9 | Karst topography | Yamaguchi MineMine, Yamaguchi 34°14′11.14″N 131°17′26.05″E﻿ / ﻿34.2364278°N 131.2905694°E﻿ / 34.2364278; 131.2905694 |
| Akiyoshi cave (秋芳洞, akiyoshidō) | — | — | 3.6, 3.9 | At 8.7 km (5.4 mi) second longest cave in Japan | Yamaguchi MineMine, Yamaguchi 34°13′40.17″N 131°18′12.32″E﻿ / ﻿34.2278250°N 131.3034222°E﻿ / 34.2278250; 131.3034222 |
| Cranes at Yashiro and their wintering place (八代のツルおよびその渡来地, yashiro no tsuru oyobi sono toraichi) | — | — | 1.2 | Hooded cranes | Yamaguchi variousShūnan and Kudamatsu, Yamaguchi 34°5′56.19″N 131°56′49.83″E﻿ / ﻿34.0989417°N 131.9471750°E﻿ / 34.0989417; 131.9471750 |
| Giant camphor tree in Kamo (加茂の大クス, kamo no ōkusu) | — | — | 2.1 | | Tokushima HigashimiyoshiHigashimiyoshi, Tokushima 34°2′27.39″N 133°55′54.92″E﻿ / ﻿34.0409417°N 133.9319222°E﻿ / 34.0409417; 133.9319222 |
| Chinese juniper at Hōshō-in (宝生院のシンパク, hōshōin no shinpaku) | — | — | 2.1 | 23 m (75 ft) high, 15 m (49 ft) circumference at ground level | Kagawa TonoshoTonoshō, Kagawa 34°29′36.11″N 134°11′49.86″E﻿ / ﻿34.4933639°N 134.1971833°E﻿ / 34.4933639; 134.1971833 |
| Yakama potholes (八釜の甌穴群, yakama no ōketsugun) | — | — | 3.9 | | Ehime KumakogenKumakōgen, Ehime 33°42′13.6″N 132°57′38.39″E﻿ / ﻿33.703778°N 132.9606639°E﻿ / 33.703778; 132.9606639 |
| Common jay at Kōchi and its habitat (高知市のミカドアゲハおよびその生息地, kōchishi no mikadoageha oyobi sono seisokuchi) | — | — | 1.2 | | Kochi KochiKōchi, Kōchi 33°33′13.06″N 133°32′24.07″E﻿ / ﻿33.5536278°N 133.5400194°E﻿ / 33.5536278; 133.5400194 |
| Giant cedars at Sugi (杉の大スギ, sugi no ōsugi) | — | — | 2.1 | Two stems, each about 16 m (52 ft) circumference | Kochi OtoyoŌtoyo, Kōchi 33°45′20.17″N 133°39′47.01″E﻿ / ﻿33.7556028°N 133.6630583°E﻿ / 33.7556028; 133.6630583 |
| Japanese Box primeval forest at Mount Kosho (古処山ツゲ原始林, koshosan tsuge genshirin) | — | — | 2.1 | | Fukuoka variousAsakura and Kama, Fukuoka 33°28′54.67″N 130°43′29.8″E﻿ / ﻿33.4818528°N 130.724944°E﻿ / 33.4818528; 130.724944 |
| Camphor tree primeval forest at Mount Tachibana (立花山クスノキ原始林, tachibanayama kusunoki genshirin) | — | — | 2.2, 2.10 | | Fukuoka variousShingū and Hisayama, Fukuoka 33°40′45.67″N 130°28′6.23″E﻿ / ﻿33.6793528°N 130.4683972°E﻿ / 33.6793528; 130.4683972 |
| Mucuna sempervirens at Aira (相良のアイラトビカズラ, aira no airatobikazura) | — | — | 2.1, 2.12 | | Kumamoto KikukaKikuka, Kumamoto 33°3′51.16″N 130°46′5.53″E﻿ / ﻿33.0642111°N 130.7682028°E﻿ / 33.0642111; 130.7682028 |
| Aoshima subtropical plant communities (青島亜熱帯性植物群落, aoshima anettai seishokubutsugunraku) | — | — | 2.2 | | Miyazaki MiyazakiAoshima, Miyazaki, Miyazaki 31°48′18.69″N 131°28′32.7″E﻿ / ﻿31.8051917°N 131.475750°E﻿ / 31.8051917; 131.475750 |
| Sago palm natural habitat at Cape Toi (都井岬ソテツ自生地, toimisaki sotetsu jiseichi) | — | — | 2.10 | | Miyazaki KushimaKushima, Miyazaki 31°21′54.78″N 131°20′24.03″E﻿ / ﻿31.3652167°N 131.3400083°E﻿ / 31.3652167; 131.3400083 |
| Mitrastema at Uchiumi (内海のヤッコソウ発生地, uchiumi no yakkosō hasseichi) | — | — | 2.12 | Mitrastema yamamotoi | Miyazaki MiyazakiMiyazaki, Miyazaki 31°44′28.97″N 131°28′3.81″E﻿ / ﻿31.7413806°N 131.4677250°E﻿ / 31.7413806; 131.4677250 |
| Yakushima primeval cedar forest (屋久島スギ原始林, yakushima sugi genshirin) | — | — | 2.2 | Includes with the Jōmon Sugi, the oldest specimen of Cryptomeria japonica | Kagoshima YakushimaYakushima, Kagoshima 30°19′40.23″N 130°31′23.06″E﻿ / ﻿30.3278417°N 130.5230722°E﻿ / 30.3278417; 130.5230722 |
| Kamō camphor tree (蒲生のクス, kamō no kesu) | — | — | 2.1 | Height: 30 m (98 ft), circumference: 24 m (79 ft) | Kagoshima KamoKamō, Kagoshima 31°45′44.38″N 130°34′11.77″E﻿ / ﻿31.7623278°N 130.5699361°E﻿ / 31.7623278; 130.5699361 |
| Origin of Kandelia obovata at Kiire (喜入のリュウキュウコウガイ産地, kiire no ryūkyōkōgai sanchi) | — | — | 2.10 | | Kagoshima KagoshimaKagoshima, Kagoshima 31°22′29.34″N 130°32′49.26″E﻿ / ﻿31.3748167°N 130.5470167°E﻿ / 31.3748167; 130.5470167 |
| Natural habitat of the sago palm in Kagoshima Prefecture (鹿児島県のソテツ自生地, kagoshimaken no sotetsu jiseichi) | — | — | 2.10 | | Kagoshima variousYamagawa, Bonotsu, Sata and Uchinoura, Kagoshima 31°21′13.09″N 130°42′15.64″E﻿ / ﻿31.3536361°N 130.7043444°E﻿ / 31.3536361; 130.7043444 |
| Cranes in Kagoshima Prefecture and their wintering place (鹿児島県のツルおよびその渡来地, kagoshimaken no tsuru oyobi sono toraichi) | — | — | 1.2 | Hooded cranes | Kagoshima IzumiIzumi, Kagoshima 32°6′9.52″N 130°16′25.75″E﻿ / ﻿32.1026444°N 130.2738194°E﻿ / 32.1026444; 130.2738194 |
| Birōjima subtropical plant communities (枇榔島亜熱帯性植物群落, birōjima anettai seishokubutsugunraku) | — | — | 2.2, 2.10 | | Kagoshima ShibushiShibushi, Kagoshima 31°25′45.3″N 131°7′1.89″E﻿ / ﻿31.429250°N 131.1171917°E﻿ / 31.429250; 131.1171917 |
| Shirouma mountain range alpine plant zone (白馬連山高山植物帯, shiroumarenzan kōzanshokubutsutai) | — | — | 2.3 | | various variousAsahi and Kurobe in Toyama; Hakuba in Nagano; Itoigawa in Niigata 36°38′56.9″N 137°44′55.73″E﻿ / ﻿36.649139°N 137.7488139°E﻿ / 36.649139; 137.7488139 |
| Ozegahara (尾瀬, oze) | — | — | 4 | | various variousYunotani, Niigata; Katashina, Gunma; Hinoemata, Fukushima 36°56′33.93″N 139°13′59.41″E﻿ / ﻿36.9427583°N 139.2331694°E﻿ / 36.9427583; 139.2331694 |
| Short-tailed albatross (アホウドリ, ahōdori) | — | — | 1.2 | | various variousOgasawara Islands (Tokyo) and Okinawa |
| Amami rabbit (アマミノクロウサギ, amami no kuro usagi) | — | — | 1.1 | | Kagoshima variousTokunoshima and Amami Ōshima, Kagoshima |
| Iriomote cat (イリオモテヤマネコ, iriomote yamaneko) | — | — | 1.1 | Endemic to one island (Iriomote) | Okinawa IriomoteIriomote, Okinawa |
| Japanese giant salamander (オオサンショウウオ, ōsanshōuo) | — | — | 1.2 | At up to 1.5 m (4 ft 11 in) length, the second largest salamander in the world | various Iriomote11 prefectures, among others: Gifu, Mie, Hyōgo, Hiroshima, Shimane, Tottori, Ōita |
| Japanese serow (カモシカ, kamoshika) | — | — | 1.1 | found on all main Japanese islands except for Hokkaidō | various various29 prefectures including Aomori |
| Otter (カワウソ, kawauso) | — | — | 1.2 | | various variousvarious |
| Crested serpent-eagle (カンムリワシ, kanmuriwashi) | — | — | 1.1 | | Okinawa variousOkinawa |
| Oriental stork (コウノトリ, kō no tori) | — | — | 1.2 | | various variousHyōgo and Fukui |
| Red-crowned crane (タンチョウ, tanchō) | — | — | 1.2 | | Hokkaido variousHokkaidō |
| Crested ibis (トキ, toki) | — | — | 1.2 | | various variousNiigata and Ishikawa |
| Okinawa woodpecker (ノグチゲラ, noguchigera) | — | — | 1.1 | Endemic to Okinawa Island | Okinawa Okinawa IslandOkinawa Island, Okinawa |
| Bonin white-eye (メグロ, meguro) | — | — | 1.1 | Endemic to the Bonin Islands | Tokyo Bonin IslandsBonin Islands, Tokyo |
| Rock ptarmigan (ライチョウ, raichō) | — | — | 1.2 | | various variousToyama, Nagano, Niigata, Yamanashi, Shizuoka, Gifu |
| Long-tailed fowl of Tosa (土佐のオナガドリ, tosa no onagadori) | — | — | 1.4 | | Kochi NankokuNankoku, Kōchi |