This is a partial list of zoos in Japan. For aquaria, see List of aquaria in Japan.

Such facilities include zoos, safari parks, animal theme parks, aviaries, butterfly zoos, and reptile centers, as well as wildlife sanctuaries and nature reserves where visitors are allowed.

• Higashiyama Zoo and Botanical Gardens, Nagoya
• Japan Monkey Centre, Inuyama, Aichi
• Okazaki Higashi Park Zoo, Okazaki, Aichi
• Toyohashi Zoo & Botanical Park, Toyohashi, Aichi
• Toyota City Kuragaike-Park, Toyota, Aichi

• Akita Omoriyama Zoo, Akita, Akita

• Chiba Zoological Park, Chiba, Chiba^[1]
• Ichihara Elephant Kingdom, Ichihara, Chiba
• Ichikawa Zoological & Botanical Garden, Ichikawa, Chiba^[2]
• Mother Farm, Futtsu, Chiba

• Tobe Zool. Park of Ehime Prefecture, Iyo, Ehime

• Sabae Nishiyama Park Zoo, Sabae, Fukui

• Assuran Bird House, Onojo
• Fukuoka Municipal Zoo and Botanical Garden, Fukuoka
• Itozu no Mori Zoological Park, Kitakyūshū
• Kurume City Bird Center, Kurume, Fukuoka
• Ōmuta Zoo, Ōmuta, Fukuoka
• Uminonakamichi Seaside Park Zoological Garden, Fukuoka

• Gunma Safari Park, Tomioka, Gunma
• Kiryugaoka Zoo, Kiryu, Gunma

• Fukuyama City Zoo, Fukuyama, Hiroshima
• Hiroshima City Asa Zoological Park, Hiroshima

• Asahiyama Zoo, Asahikawa, Hokkaidō
• Kushiro Zoo, Kushiro, Hokkaidō
• Noboribetsu Bear Park, Noboribetsu, Hokkaidō^[3]
• Obihiro Zoo, Obihiro, Hokkaido
• Sapporo Maruyama Zoo, Sapporo^[4]

• Awaji Farm Park England Hill, Minamiawaji, Hyōgo
• Himeji Central Park, Himeji, Hyōgo
• Himeji City Zoo, Himeji, Hyōgo
• Kobe Kachoen, Kobe
• Oji Zoo, Kobe

• Hitachi Kamine Zoological Garden, Hitachi, Ibaraki

• Ishikawa Zoo, Nomi, Ishikawa

• Morioka Zoological Park, Morioka, Iwate

• Amami Islands Botanical Garden, Kagoshima
• Hirakawa Zoological Park, Kagoshima

• Kanazawa Zoological Gardens, Yokohama
• Nogeyama Zoo, Yokohama
• Odawara Zoo, Odawara, Kanagawa
• Yokohama Zoo (Zoorasia), Yokohama
• Yumemigasaki Zoological Park, Kawasaki, Kanagawa

• Noichi Zoological Park of Kōchi Prefecture, Komi District, Kōchi^[5]
• Wanpark Kōchi Animal Land, Kōchi, Kōchi

• Cuddly Dominion, Aso, Kumamoto
• Kumamoto City Zoological and Botanical Gardens, Kumamoto, Kumamoto

• Kyoto Municipal Zoo, Kyoto

• Miyagi Zao Fox Village
• Yagiyama Zoological Park, Sendai

• Miyazaki City Phenix Zoo, Miyazaki, Miyazaki

• Iida City Zoo, Iida, Nagano
• Nagano Chausuyama Zoo, Nagano, Nagano
• Omachi Alpine Museum, Omachi, Nagano
• Suzaka Zoo, Suzaka, Nagano

• Nagasaki Biopark, Saikai, Nagasaki
• Sasebo Zoological Park and Botanical Garden, Sasebo, Nagasaki

• Kyushu Natural Animal Park African Safari, Usa, Ōita
• Takasakiyama Natural Zoological Garden, Ōita, Ōita

• Ikeda Zoo, Okayama, Okayama
• Great Ape Research institute, Hayashibara, Tamano, Okayama

• Neo Park Okinawa, Nago, Okinawa
• Okinawa Kodomo Future Zone, Okinawa

• Kashihara City Insectary Museum, Kashiwara, Osaka
• Misaki Koen, Sennan, Osaka
• Satsukiyama Zoo, Ikeda, Osaka
• Tennoji Zoo, Osaka

• Miyazawako Nakayoshi Zoo, Hannō, Saitama
• Saitama Children's Zoo, Higashimatsuyama, Saitama
• Saitama Omiya Park Zoo, Saitama, Saitama
• Sayama Chikosan Park Children Zoo, Sayama, Saitama
• Tobu Zoo, Minamisaitama District, Saitama

• Matsue Vogel Park, Matsue, Shimane

• Atagawa Tropical & Alligator Garden, Kamo District, Shizuoka
• Fuji Safari Park, Susono, Shizuoka
• Hamamatsu Municipal Zoo, Hamamatsu
• iZoo, Kawazu, Shizuoka
• Izu Biopark, Kamo District, Shizuoka
• Izu Shaboten Zoo, Itō, Shizuoka
• Mishima City Park Rakujuen, Mishima, Shizuoka
• Shizuoka Municipal Nihondaira Zoo, Shizuoka, Shizuoka

• Nasu Animal Kingdom, Nasu, Tochigi^[6]
• Utsunomiya Zoo, Utsunomiya, Tochigi

• Tokushima Municipal Zoo, Tokushima, Tokushima

• Edogawa Ward Natural Zoo, Edogawa, Tokyo
• Hamura Zoological Park, Hamura, Tokyo
• Inogashira Park Zoo, Tokyo
• Ōshima Park Zoo, Izu Ōshima^[7][8]
• Tama Zoo, Tokyo
• Ueno Zoo, Ueno, Tokyo
• Adachi Park of Living Things , Adachi, Tokyo

• Takaoka Kojo Park Zoo, Takaoka, Toyama
• Toyama Municipal Family Park Zoo, Toyama, Toyama

• Adventure World, Shirahama, Shirahama, Wakayama [1]
• Wakayama Park Zoo, Wakayama, Wakayama

• Akiyoshidai Safari Land, Mine, Yamaguchi
• Shunan Municipal Tokuyama Zoo, Shūnan, Yamaguchi
• Ube Tokiwa Park, Ube, Yamaguchi

• Kofu Yuki Park Zoo, Kofu, Yamanashi

• List of aquaria in Japan
• List of botanical gardens in Japan
• List of dolphinariums
• List of fossil parks
• List of national parks
• List of tourist attractions worldwide
• List of WAZA member zoos and aquariums
• List of wildlife sanctuaries
• List of zoos

• "List of Zoos" (PDF). jazga.or.jp. Japanese Association of Zoos and Aquariums. Retrieved 12 June 2010.^{[permanent dead link‍]}