Daisen-in, a subtemple of Daitoku-ji was founded in 1509 by Zen priest Kogaku Soko1464-1548. The gardens date from about that time and may have been designed by Kogaku or perhaps by the painter Soami, who did the landscape paintings in the main hall. The garden is a miniature landscape with mountains, waterfalls and river and wraps entirely around the main hall, hojo.
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.