
The Aloha Garden Tateyama is a botanical garden located in Tateyama, Chiba, Japan. It is open daily; an admission fee is charged.

The Himeji City Tegarayama Botanical Garden , also known as the Himeji Tegarayama Green House, is a botanical garden located within a greenhouse in Tegarayama Central Park at 93 Tegara, Himeji, Hyogo, Japan.

The Itabashi Botanical Garden is an indoor botanical garden located at 8-29-2 Takashimadaira, Itabashi, Tokyo, Japan. It is open daily except Mondays. It was closed to start renovation work in September 2020 and reopened on April 20, 2021.

The Kiseki No Hoshi Greenhouse , also known as the Miracle Planet Museum of Plants, is a botanical garden within a greenhouse located at Yumebutai 4 Banchi, Higashiura-cho, Tsuna, Awaji, Hyōgo, Japan. It is open most days; an admission fee is charged.

Kobe Animal Kingdom is an animal and flower park located on Port Island in Kobe, Japan. It is mainly located in and around a greenhouse. It was called Kobe Kachoen until 18 July 2014. It is one of several theme parks created by Japanese botanist and collector Kamo Mototeru, and was opened on 15 March 2006. This all-weather park is based on the concept of contact with birds and flowers. In the park, visitors are able to touch and feed birds.

The Kyoto Botanical Garden , also known as the Kyoto Prefectural Botanical Garden, is a major botanical garden with conservatory located next to the Kamo River, Hangi-cho Simogamo, Sakyō-ku, Kyoto, Japan. It is open daily; an admission fee of 200 yen is charged, and an additional fee of 200 yen is charged for accessing the conservatory.

Nagasaki subtropical botanical garden It is a botanical garden that was in Wakimisakimachi 833, Nagasaki, Nagasaki, Japan. Nagisaki Town, a subtropical botanical garden in Nagasaki City, was closed on March 31, 2017 and completed operation for 47 years. In the closing ceremony, volunteer leaders and members of the local residents' association also participated and missed parting with the garden which contributed to the revitalization of the area for about half a century.

The Nunobiki Herb Garden is a herb garden located on Mount Rokkō above Kobe, Japan. It is open daily; an admission fee is charged.

The Sakuya Konohana Kan (咲くやこの花館) is a botanical garden set within one of the world's largest greenhouses, located in Tsurumi Ryokuchi park at 2-163 Ryokuchi Koen, Tsurumi-ku, Osaka, Japan. It is open daily except Mondays; an admission fee is charged.

The Shinjuku Gyo-en Greenhouse is a greenhouse in Shinjuku Gyo-en, Shinjuku, Tokyo, Japan. It was built in 1950 and displays more than 1,700 tropical and subtropical plant species, as of 2016.

The Suma Rikyu Park is a park with botanical garden located at Higashi Suma 1-1, Suma-ku, Kobe, Hyōgo, Japan. It is open daily except Thursdays; an admission fee is charged.

The Tsukuba Botanical Garden is a major botanical garden near the University of Tsukuba at 4-1-1 Amakubo, Tsukuba, Ibaraki Prefecture, Japan. It is open daily except Mondays; an admission fee is charged.

The Yumenoshima Tropical Greenhouse Dome , also sometimes called the Yumenoshima Tropical Plant Dome, is a botanical garden located at 3-2, Yumenoshima, Kōtō, Tokyo, Japan. It is operated by the Tokyo Metropolitan Park Association and open daily except Mondays; an admission fee is charged.