The aim of this study was to propose a method for site selection for habitat conservation or restoration of threatened freshwater fishes inhabiting ditches or canals in the main plains of northern Kyushu Island, Japan. The environmental data of 4,084 third meshes in six regions and faunal data of 337 meshes that included 462 sites were analyzed using generalized liner mixed models, and species distribution models with high accuracies were developed for nine threatened species. Habitat conservation or restoration for each species was discriminated using gaps between actual and potential distributions. The number of species under each management was determined for each site, and the management type with a large number of species was selected (Case 1), or the target species were set for each potential faunal group based on similarities of fish fauna, and the type was selected by counting only the target species (Case 2). On the basis of the conserved sites showing actual presences, Case 2 showed higher effectiveness than Case 1. The estimated practices and successes of all habitat managements in Case 2 showed an increase of 1.3–4.6 times for actual presences, with optimal habitats reaching 78–91 % of their potential presence and conserved sites attaining 64–97 % of the actual presence of each species. In the case with special attention to the most threatened species, Acheilognathus tabira nakamurae, a small decrease in effectiveness was noted for several species.
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