Chagusaba, which is traditional tea-grass integrated system in Shizuoka, is one of Globally Important Agricultural Heritage Systems (GIAHS) sites in Japan. Chagusaba provide an important habitat for natural plant species. In this study, we investigated the flora in Chagusaba and environmental factors to affect the number of native species estimated their diversity. Fifty Chagusaba were classified in to five vegetation types by Two-way indicator species analysis. In addition, high number of native plant species Chagusaba had low soil pH, covered large areas, and were in places where the land had not been modified. Through statistical analysis (GLM), we found that land modification had an especially significant effect on the diversity of native plants, and that the diversity of native plants was reflected in the history of the use of the land.