In order to conserve and restore the habitat of a species for sustaining biodiversity, information on the species occurrence is essential, but there is little data regarding this. Producing a potentially suitable habitat (PSH) map is helpful for decision makers and land developers to establish strategies for conservation and for avoiding conflict of land use. The aims of this study are to i) establish a model for predicting PSH of endangered hygrophytes from species-occurrence data and several environmental variables, and ii) evaluate the degree of habitat loss in Tokushima Prefecture. The method for finding PSH is as follows; 1) Distribution data of target species are collected from specimens in the prefectural museum and field survey, and input into a GIS database. 2) Through CCA and cluster analysis, 66 target species are classified into ecological groups by using environment variables (stream power index, topographical wetness index, slope inclination, precipitation, elevation, etc.), and then factors limiting the occurrence of species group are identified using the index of electivity. 3) Areas with the same environmental sets preferred by each group are selected from entire region of Tokushima, and then potentially suitable habitat is found by overlaying the layers of selected areas. Geomorphologic characteristics of the PSHs of group A-D are as follows; the PSH of group-A is found at headwaters in mountain regions with gentle slope. The PSH of group-B corresponds with the area of flood plain formed by the Yoshino River. It is considered that temporary wetlands used to be created by frequent floods. Alluvial lowland areas around the mouths of Yoshino and Naka River acted as the PSH of group-C. The area is young, as it was formed within the last 6000 years after decrease of sea water level. The PSH of group-D is composed of various geomorphic types from lowland to mountain, and high areal ratio of gravel and rocky terraces is the characteristic of the area. Among group-D, it is considered that wetlands, which used be formed on the border between flood plain and terrace are the PSH of group-D1, and temporal wetlands formed at eroded areas are the PSH of group-D2. The area of PSHs of group B and C have been widely used as paddy fields and residential areas, and modernization of irrigation system and urbanization is ongoing. Thus the risk of extinction of the hygrophytes species is extremely high compared to the other three groups.