Paddy fields are important habitats for plants and animals that occur in wet habitats. However, changes in environment in rice field (e.g., farmland consolidation) have caused great decrease in the diversity of these species. To advance the conservation of these species, we examined useful bio-indicators for habitat quality in rice fields. The study sites were located in in Kami-ina District, Nagano Prefecture, central Japan. These study sites were classified into 4 landscape types; mountainous non-consolidated, mountainous consolidated, urban non-consolidated, and urban consolidated. In each site, we recorded floristic diversity, and measured water quality, soil moisture, land use, and management types. A total of 62 species including 11 endangered species were identified from the survey. The species richness was higher in mountainous area compared to that in urban area. Notably, the occurrence of several species was deeply related to wet condition. Considering that humid condition is essential for some endangered species in rice fields, these species can be used as bio-indicators for conservation of these species vulnerable to desiccation.