List of Ramsar Convention sites
- Akan-ko
- Akiyoshidai Groundwater System
- Akkeshi-ko and Bekambeushi-shitsugen
- Arao-higata
- Biwa-ko
- Fujimae-Higata
- Furen-ko and Shunkuni-tai
- Higashiyoka-higata
- Hinuma
- Hizen Kashima-higata
- Hotokenuma
- Hyo-ko
- Imuta-ike
- Izu-numa and Uchi-numa
- Kabukuri-numa and the surrounding rice paddies
- Katano-kamoike
- Kejo-numa
- Keramashoto Coral Reef
- Kiritappu-shitsugen
- Kuju Bogatsuru and Tadewara-shitsugen
- Kushimoto Coral Communities
- Kushiro-shitsugen
- Kutcharo-ko
- Lower Maruyama River and the surrounding rice paddies
- Manko
- Mikata-goko
- Miyajima
- Miyajima-numa
- Nagura Amparu
- Nakaikemi-shicchi
- Nakaumi
- Notsuke-hanto and Notsuke-wan
- Oku-Nikko-shitsugen
- Onuma
- Oyama Kami-ike and Shimo-ike
- Oze
- Sakata
- Sarobetsu-genya
- Shinji-ko
- Streams in Kume-jima
- Tateyama Midagahara and Dainichidaira
- Tofutsu-ko
- Tokai Hilly Land Spring-fed Mires
- Uryunuma-shitsugen
- Utonai-ko
- Watarase-yusuichi
- Yakushima Nagata-hama
- Yatsu-higata
- Yonahawan
- Yoshigadaira Wetlands
List of World Heritage Convention sites
- Buddhist Monuments in the Horyu-ji Area
- Fujisan, sacred place and source of artistic inspiration
- Gusuku Sites and Related Properties of the Kingdom of Ryukyu
- Himeji-jo
- Hiraizumi – Temples, Gardens and Archaeological Sites Representing the Buddhist Pure Land
- Hiroshima Peace Memorial (Genbaku Dome)
- Historic Monuments of Ancient Kyoto (Kyoto, Uji and Otsu Cities)
- Historic Monuments of Ancient Nara
- Historic Villages of Shirakawa-go and Gokayama
- Itsukushima Shinto Shrine
- Iwami Ginzan Silver Mine and its Cultural Landscape
- Ogasawara Islands
- Sacred Sites and Pilgrimage Routes in the Kii Mountain Range
- Shirakami-Sanchi
- Shiretoko
- Shrines and Temples of Nikko
- Sites of Japan’s Meiji Industrial Revolution: Iron and Steel, Shipbuilding and Coal Mining
- Tomioka Silk Mill and Related Sites
- Yakushima