Zuiho-in is a subtemple of Daitoku-ji in Kyoto. It was founded in 1546 by Sorin Otomo, a daimyo who later converted to Christianity. The current gardens were designed by Merei Shigemori in 1961, and the smaller north garden has a rock arrangement in the shape of a cross as a memorial to Sorin. The temple became associated with the tea masters Sen no Rikyu and Kobori Enshu ,also a great garden designer.
Daitoku-ji is a complex of 24 sub-temples, and a main center of Rinzai Zen Buddhism. If you have only one day in Kyoto, Daitoku-ji would provide a good overview of zen temples and gardens.