https://www.bonsai-art-museum.jp/en/
Please give me some time to look into the others.
Discussion
Thank you my fren 🙏
The most popular garden in Japan. It's quite far from Tokyo.
It's Kokedera in Kyoto. You need to make a reservation in advance to visit.
A bonsai garden in Kyoto.
I found a travel guide for Kyoto, in case you need it.