The aim of this study is obtain the character of the rock garden of the Nikko botanical gardens attached to Tokyo Imperial University in the foundation period (1902-1911). Not just as the research facility of alpine plants, as the shelter, Nikko botanical gardens were founded at Hotokeiwa, near the Nikko Toshogu Shrine, in 1902 by Prof. Jinzo Matsumura. In the botanical gardens, the rock garden was gradually made. This rock garden featured some hill tastefully arranged with a cascade, running water and stones. The growth of the alpine plants in the rock garden was good. The botanical gardens were open to public from about 1906. The Nikko botanical gardens moved to Rengeishi because of small site (2,620 tsubo) and floods, but are important as a monumental birthplace of the real rock garden in the modern botanical gardens of Japan.