In recent years, paddy fields have become important environment as alternative habitats for freshwater organisms. Although most of paddy weeds were once very common, now they have become endangered in Japan. However, we have few basic data (e.g., location, the paddy weeds communities and the relationship between those communities and environmental conditions) to conserve them. Therefore, by clarifying the relationship between environmental conditions and the structure of paddy weeds communities, this study aim to consider conservation measures for threatened species, in the mountainous areas containing abandoned farmlands. We carried out vegetation survey at 40 rice fields in Nagano Prefecture, central Japan, during the weed-growing season. And we carried out environmental condition survey (location, pH and soil moisture content at plots of soil and paddy management) during non-irrigation season in 2011. The number of appearance species was 95. And there were including of 15 threatened species. These threatened species had submerged plants (e.g., Blyxa japonica, Chara spp.) and emerged plant (e.g., Leersia japonica), amphibious plant (e.g., Deinostema violaceum). For the meeting, we want to discuss with further results.