In the last century, modern and intensive agriculture have reduced biodiversity in farmland in the countries where have long histories of agriculture. On the other hands, agriculture is the typical human activity to use biodiversity and ecosystem services. Agriculture needs many types of ecosystem services such as microorganism for fertile soil, insects and other animals as pollinators or natural enemies, forest for groundwater occurrence. Some of these ecosystem services depend on landscape structure around agricultural fields. Therefore farmers have adequately maintained biodiversity and ecosystem in and around farmland. Based on these backgrounds, I want to introduce our research activities about the relationship between agriculture and biodiversity in rural landscape, for example, historical changes of rural landscape and its effect on biodiversity in Japan, especially Satoyama and paddy dominated landscape, landscape mosaic which maintained by farmers’ management around Yatsu paddy fields, Satoyama resources uses in tea production, and natural enemies’ habitation around paddy fields. Finally, I want to discuss about rebuilding of the relationship between agriculture and biodiversity with importance of sustainable use of rural resources.